Tag: CDS

A viral pan-end RNA element and host complex define a SARS-CoV-2 regulon

Cell lines and culture A549-hACE2 [a gift from Dr. Ben tenOever3], 293 T, HEK293, A549, and 3T3-L1 pre-adipocyte cell lines (refer to Supplementary Table 1) were cultured in DMEM and 10% FBS. U937, Calu-3, and HCT116 cells were cultured in RPMI, EMEM, and McCoy’s 5 A media, respectively, with 10% FBS. Caco-2 cells…

Continue Reading A viral pan-end RNA element and host complex define a SARS-CoV-2 regulon

As expected, wine grapes found to have high deleterious genetic burden

A region containing a Fer-like gene was predicted to have introgressed from the EU and under selection. (A) A cluster of the malectin/receptor-like protein kinase domain was observed around the introgressed region. The malectin domain is represented by blue boxes. The red boxes indicate the CDS of the candidate Fer-like…

Continue Reading As expected, wine grapes found to have high deleterious genetic burden

RefSeq: NC_010572 CDS #2537

RefSeq: NC_010572 CDS #2537 >NC_010572 (refseq) 3006597..3008225 /translation= MDLVLRDALVVDGTGAPSYRADVALDGGRIAEIHPEGSPGPRPTAARTVDADGLALAPGF IDMHAHSDLALLRDPDHSAKAAQGVTLEVLGQDGMSYAPADDRTLAEVRRSITGWNGDGS DIDFDWRTVGGYLDRLDRNFGGQGIAVNAAYLVPQGTVRMYAVGWDDRPATTAELARMKE LVDQGMREGAVGLSSGLTYTPGMYADDAELTELCRVVARHGGYYCPHHRSYGAGALEAYE EMVLLTRNAGCALHLAHATMNFGVNKGRAPDLLALLDGALAAGADISLDTYPYTPGCTTL VAMLPSWASEGGPESVLTRLADPASAERIRHHLEVLGSDGCHGVPIEWDTIEISGVSVPH LGEYVGRTVEESARLRGEEPWVTARRLLTEDRLGTTILQHVGHEENVQQIMRHPVHTGGS DGILQGDKPHPRAYGTFPQYLGRYARELGILSLEECVAHLTSRPAARLRLADRGLVREGY RADLVLFDPETVAAGSTFEEPRTLPVGIPHVLIDGRFVIEDGKRTSVLAGKAVRGAGAAA TA BLAST Read more here: Source link

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RefSeq: NC_014008 CDS #1128

RefSeq: NC_014008 CDS #1128 >NC_014008 (refseq) complement(1493788..1495038) /translation= MLKRYLKWVLPVFFTAFLLASVIARPDFRALFSLEFWESLQRYSRVMRLVEAEYVHADEV SFPGLTDNALKQAVHSLDRYSRYMTPEDYTDYTMISNQEYVGVGILIEQFAGQVTIAEVF DGGAAAGAGMMAGDLIVGVDQEDVEGEDLSEISNRIRGEPGTAVQLQIQRPNVAERIDFE LERGAITLAAVSQQELRADAIAYLKMTQFTDQADEEIEAVLADLQAEGMRGLILDLRGNP GGRLDTAANIASCFLDPGQLIVTIEARRGVVEQIRSERSDLRVTQPLVILIDGSSASASE ILAGALRDHGRAVLVGAQSFGKGTVQSVFGFNDGTGLKLTTARYLLPNGEAINGTGVEPD VEVALTDEERYIKMLQKHHLRTMDAIRFEQRFGFAPVEDRALELAEHLLLGRLAQE BLAST Read more here: Source link

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acCRISPR: an activity-correction method for improving the accuracy of CRISPR screens

acCRISPR framework acCRISPR performs essential gene identification by calculating two scores for each sgRNA, namely the cutting score (CS) and the fitness score (FS). CS and FS are the log2-fold change of sgRNA abundance in the appropriate treatment sample with respect to that in the corresponding control sample (see Supplementary…

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Vancomycin intermediate-resistant Staphylococcus haemolyticu | IDR

Wanyang Dong,1,* Qi Peng,1,* Xiaohua Tang,1,2,* Tian Zhong,1 Shunan Lin,1 Ziling Zhi,1 Jingyi Ye,1 Bixia Yang,1 Ning Sun,1,3 Wenchang Yuan1 1Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, 510180, People’s Republic of China; 2Third Affiliated Hospital…

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RefSeq: NC_004578 CDS #1657

RefSeq: NC_004578 CDS #1657 >NC_004578 (refseq) complement(1792171..1794648) /translation= MRVFYWTLRALLSHWRRHPVQFFSVLTGLWLATALLTGVQALNSQARESYQRASQLIGGE PQTSIAAPDGGLFAQELYIQLRREGWPVSPVIRGRITLKGLEGQRLQLLGIEPLTLPNST LAGQTLDSDQVVDFLTPPGATWVSPQTLESLGLEEGRQPLGENGVALPPLRAKPDMAPGV LLTDIGFAQALLGQPDELSSLLLHKDFAARNPQLPPALNGQLVISKTGEENNLQRLTESF HLNLSALGVLSFGVGLFIVHAAIGLALEQRRGLLRNLRACGVSARMLITALSVELGAMAL LGGLLGVVSGYFLASLLLPDVVASLRGLYGAEVAGQLNLSLWWWLSGIGLSLLGALLAGI NSLLRAARLPLLALADAQAWQQAHARWLRRQAWVAAAGALVALLALLFGNSLLLGFVLMS AVLFSAGLGLPVLLDAMLGGLLTRSRSVLGQWFLADCRQQLPSLSLALMALLLAMAANIG VGSMTSGFRQTFNSWLNQRLTAELYVSPQDPTQAQPLQTWLSQQAHISAVIPNWQVAVQV QGWPADLFGVVDHTIYRQHWELLESVKGDPWNLLRDGDTVMLSEQLARRLKLTLNDTLNI PVPNGQWTPRIVGIYADYGNPKGHLLVNEKHLLAHWPQLSPFRFNLRVDQAAIPPLVKQL QDRFALDDNHIIDQSQIKRWSTQIFERTFSATAALNSLTLGVAGVALFISLLTQSQSRLG QLAPLWALGVTRRQLMLLNLGQTWLLALLTLAFSIPLGLMIAWCLDAVINVQAFGWRLPL QVFPLQLLQLMSLAILATLLASAWPLLKLYRSRPADLLRTFASEH BLAST Read more here: Source link

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Characterization of nuclear DNA diversity in an individual Leymus chinensis

Introduction The definition of an individual organism, traditionally defined by the invariable presence of a physiological unit and genetic homogeneity, is challenged by situations such as intraorganismal genetic heterogeneity (IGH), which refers to the presence of more than one genotype in a single organism (Schweinsberg et al., 2015). Cells within a…

Continue Reading Characterization of nuclear DNA diversity in an individual Leymus chinensis

RefSeq: NC_008787 CDS #1549

RefSeq: NC_008787 CDS #1549 >NC_008787 (refseq) complement(1575097..1576365) /translation= MSNSVTITDNRNGKSYEFPIYDGTTGPSVVDMSSFYKQTGMFSYDEGLTSTATCKSKITY IDGENGILMHRGYPIEWLAENKLYLDVVHLLLYKELPDATRLEAFRYEMKKRSFIHEGMH RLFDSFPDNAHPMAVLQGAVSSLSAFYPDHLNMNVKEEYMEMAARIVAKIPTIAATAYRY KHGFPMAYPNLDRGFTENFLYMLRTYPYDHVELKPIEVKALDTVFMLHADHEQNASTSTV RAVGSTHAHPYACIAAGIGALWGHAHGGANEGVIRMLEQIGSVDRVDEFIKRAKDKNDPF RLMGFGHRVYKNFDPRAKVLKKLRDQLIDELGIDTNLIKVATRIEEIALSDDYFVQRGLY PNVDFHSGLILKALGIPNEMFATLFVIGRTPGWIAQWIEQKEQESLKIVRPRQLYLGETS KI BLAST Read more here: Source link

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RefSeq: NC_008787 CDS #727

RefSeq: NC_008787 CDS #727 >NC_008787 (refseq) complement(741289..742563) /translation= MYLQISDLKKELILKKGILHFDFTASALALKCVEKEISKILPTYANTHSDSSLNSFKTQQ TYEQARKDIKKSLSLDENFALIACGTGSSSAIKKFQELIGIYIPPLVKERYFTQIDKNTL PLVIVGPYEHHSNELSFREGLCECIRIPLDKNGEIDFDFLEKTLQKNKKRKIIASFSLAS NVTGILSDYKRISEMVRKFKGIVAFDASSFIPYKNISCQYYDALFISSHKLIGGIGGSGL LAIKKDLCGNKPSFAAGGTVGYVSRTSQCYLCNEEALEEGGTPGILQLIRASLAFKIKDS IGVKNIEKKEEILKDYFFEKLKTIPNLILYAKNLKTRLPIFAFNIKGISPFDIAYELSKK YHIETRAGCACAGPYGHDLLGLKDNQKLKTKPGWLRISLHYTHEKENIDYFFNALNKTIV KLSH BLAST Read more here: Source link

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RefSeq: NC_004578 CDS #2444

RefSeq: NC_004578 CDS #2444 >NC_004578 (refseq) 2679127..2680236 /translation= MIQEGVAGKRPFAGARFHDEIERTAALIACRVFNAEHANLQPHSCSQANQSVYHALLEPG DNVLALNFKAGGHLTHGHKVNFSGMFFNFRHYGVDEATDLIDYDLAEQDAIRFKPKLIVC GSSSYPRLFDARRLREISDKVGALLMFDLSHEAGLIACGAIPNPVPLADVATMSMDKTMR GAHGAIILCTAKIAQKIDKGVHPGTQSSFPISRLTQTAQALLHSQTAEFREYANRVLDNA LLLEQHFLCIPNLLVTGGTDKHYLVLNTKAAFGIDGVLAEQRLEAISVLSSRQTLPGDRT SRIDDAGGIRLGTAWITSRGYELDEVSALATIIIEALSPSFDDAKKHHLLSRVNTLIATD KPKDVWRNS BLAST Read more here: Source link

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RefSeq: NC_008787 CDS #748

RefSeq: NC_008787 CDS #748 >NC_008787 (refseq) 763190..764602 /translation= MKLVESRNVNNVSSFKEALINPNAPEGGLYSPLNLPIFEGEKYANLSYKDFALKLIESFG FGEEELFKKALKSYESFDDKNTPISLQKISEKTYINELWHGPTRAFKDMALQPFGVLLSE FSKDKNILIICATSGDTGPATLKSFENAKNVKVACMYPKGGTSGVQELQMRALDKDNLKV FAIDEDFDAAQRTLKELLFSKDFQNEIKALNYELCAANSVNFGRILFQIIYHYYASLKLF NEFLEEVQIIVPSGNFGNALGAFYAKKMGAKISKIKIASNANNILSEFFNQGVYDLREKS LKKTISPAMDILISSNIERLLFAKFKDKRTKELMNLLKNERYFKLEKEELQSLQEDFEAD FCTDEECMQFIKQSKILIDPHTATCFKMLDPLKPSIITSTAEWTKFTPSMIKALYDRDSK NEKEDLKFIAKEFNVQVKDEILALFDLKNSDEKVFEARNIKKEILDWMQK BLAST Read more here: Source link

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How to sort gff3 according to chromosome order?

How to sort gff3 according to chromosome order? 1 Hello, Curious to know on how to sort the gff3 file according to its chromosome while keeping its parent (gene) and child features (mRNA, cds and exon) intact: input example: Chr6 EVM gene 212579245 212580018 . + . ID=evm.TU.Chr6.3631;Name=EVM prediction Chr6.3631…

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Whole-genome sequencing of Listeria monocytogenes isolated from the first listeriosis foodborne outbreak in South Korea

Introduction Although globalization has provided opportunities for consumers to enjoy a wide range of products and expanded global food trade, the complexity of the international food supply has contributed to an increase in foodborne outbreaks (Quested et al., 2010; Hussain and Dawson, 2013). Worldwide efforts have ensured food safety by…

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Named Server and unique Workdirectories – JupyterHub

Is there somehow possible to define individual working directories for each named server?(e.g. /home/jupyter-USERNAME/Servername/) The background is that I would like to use a named server for each project I am working on and only have access to the data for this project. Currently, all Named Servers use the same…

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Chromosome-level genome assemblies from two sandalwood species provide insights into the evolution of the Santalales

Genome sequencing and assembly We sequenced and assembled genomes for the sandalwood species S. album and S. yasi (Fig. 1). In total, ~23 Gb and ~25 Gb of clean short reads of S. album and S. yasi were obtained for the genomic survey, respectively (Supplementary Tables 1 and 2). According to k-mer analysis, the…

Continue Reading Chromosome-level genome assemblies from two sandalwood species provide insights into the evolution of the Santalales

Molecular evolution and phylogenomic analysis of complete chloroplast genomes of Cotinus (Anacardiaceae)

Abstract Cotinus is an oligo‐specific ornamentally valuable genus with a disjunct distribution in the Northern Hemisphere. Traditionally, the taxonomy of Cotinus was mainly based on leaf morphological characteristics. However, the limited availability of genomic information greatly hindered the study of molecular evolution and phylogeny of this genus. This study sequenced…

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snpEff error. No CDS checked

snpEff error. No CDS checked 0 I am building a database for genome annotation of dogs’ WES. I follow snpEff instructions from here My gtf, fasta, cds files are all from the same source here However, in Step 3 (checking database) I get an error that transcript IDs from the…

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The Advantages and Challenges of AlphaFold 2 | DNASTAR

Why is this guide focusing on AlphaFold 2, an algorithm that has only competed in and won a single CASP experiment? After all, I-TASSER — called Zhang or Yang-Server in the CASP events — has won more than any other algorithm. While I-TASSER has many merits and forms the basis…

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A previously uncharacterized Factor Associated with Metabolism and Energy (FAME/C14orf105/CCDC198/1700011H14Rik) is related to evolutionary adaptation, energy balance, and kidney physiology

Statement on ethical considerations All animal work was approved and permitted by the Local Ethical Committee on Animal Experiments and conducted according to the Guidelines for Animal Experimentation recommendations (ARRIVE guidelines). In particular, mouse work related to C57BL/6NCrl mice was approved and permitted by the Institute of Molecular Genetics of…

Continue Reading A previously uncharacterized Factor Associated with Metabolism and Energy (FAME/C14orf105/CCDC198/1700011H14Rik) is related to evolutionary adaptation, energy balance, and kidney physiology

Perl. How to extract CDS and gene sequence in a specified interval from GenBank files?

I’m a complete beginner at Perl and don’t have the slightest idea on how to do this task. I feel completely defeated. The script I’m supposed to make has to: Work with any GenBank file provided (.dat). Analyze a given interval of nucleotides in a GenBank file (specified as ARGV[0],…

Continue Reading Perl. How to extract CDS and gene sequence in a specified interval from GenBank files?

ASM2073556v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::02/11/2023 00:54:09 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::6.4 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA Genes (total)::2,705 CDSs (total)::2,642 Genes (coding)::2,580 CDSs (with protein)::2,580 Genes (RNA)::63 rRNAs::3, 3, 3 (5S, 16S, 23S) complete rRNAs::3, 3, 3…

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ASM1659215v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::12/19/2022 02:53:16 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::6.3 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA Genes (total)::4,815 CDSs (total)::4,761 Genes (coding)::4,416 CDSs (with protein)::4,416 Genes (RNA)::54 rRNAs::2, 2, 2 (5S, 16S, 23S) complete rRNAs::2, 2, 2…

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ASM386249v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::11/29/2018 17:00:26 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.7 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::3,547 CDSs (total)::3,497 Genes (coding)::3,340 CDSs (with protein)::3,340 Genes (RNA)::50 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1 (5S,…

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ASM338361v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::07/05/2018 17:04:05 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::4.5 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::5,756 CDS (total)::5,710 Genes (coding)::5,642 CDS (coding)::5,642 Genes (RNA)::46 rRNAs::2, 4, 1 (5S, 16S, 23S) complete rRNAs::2, 1, 1 (5S, 16S,…

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How do you add an ORF that overlaps the two regions where a circular genome is cut in Genbank?

How do you add an ORF that overlaps the two regions where a circular genome is cut in Genbank? 1 Dear Biostars community, I had a question regarding the BankIt (Genbank) submission for circularized genomes. Let’s say I have a circularized genome from 1 to 100000 bp. And I also…

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PhaeoEpiView: an epigenome browser of the newly assembled genome of the model diatom Phaeodactylum tricornutum

Despite being an established model, the genome and annotation of P. tricornutum are not concordant and the existing epigenetic resources generated so far lack a well-defined framework for accurate and user friendly utilization. To address this limitation, we sought to establish a coherent resource rendering the multiple genomic and epigenomic…

Continue Reading PhaeoEpiView: an epigenome browser of the newly assembled genome of the model diatom Phaeodactylum tricornutum

DNA Printing, Bioengineered Kidney Constructs in Space, Revvity’s Big Pharma Agreements, More

May 24, 2023 | The Association for Molecular Pathology releases recommendations for germline variants detected by NGS, 10x Genomics wins German injunction against NanoString Technologies, and Revvity—formerly PerkinElmer—announces new license agreement with AstraZeneca. Plus new products and deployments from DNA Script, Thermo Fisher, Model N, GenScript, and more. Clear Labs…

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Peaks annotation on bacterial genome

Peaks annotation on bacterial genome 1 Hi all, I’m trying to annotate peaks identified in ChIP-seq experiments in M. tuberculosis using ChIPpeakAnno on R. I would like to distinguish between peaks that are located in promoter regions or in coding regions. Is it that possible? Is there any code I…

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extracting gencode 3utr and 5utr as part of R pipeline

Hello, I reviewed this link 3utr/5utr extraction from Gencode, I want to change and adapt the code as part of an R pipeline, where the genes$type field is replaced. I tried to adapt the code, so it encompassed all UTRs not just protein coding. working_directory_path <- getwd() library(GenomicRanges) # From…

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RefSeq: NC_015666 CDS #509

RefSeq: NC_015666 CDS #509 >NC_015666 (refseq) complement(517400..518839) /translation= MALSVLLEAVLAAFEAPVVGLEIDRSMVTILGLITIVILIALSGFFSSSEIAMFNLPKHR IEGMVEEGVDRAELVETLKSDPHRLLVTILVGNNLVNIAMSSIATALLGLYFESGLTPVL LSTFGVTAIVLLFGESVPKSYAVENTESWSLSVSRPLKVTEYVLYPLIIVFDYLTRQVNR LIGSSGAIESPYVTRDEIQEMIESGEREGVLEEDEHEMLQRIFRFNNTIVKEVMTPRLDM TAVPKDASIDEAIETCIQSGHARIPVYEGSLDNVMGVVHIRDLVRDLNYGETNDGDLELA DLIQPTLHVPESKNVDELLTEMRENRMHMAIVIDEFGTTEGLVTMEDMVEEIIGEILEGG EEQPIEEIDERTVLVRGEVNIEDVNEALEIDLPEGEEFETIAGFIFNRAGRLVEEGEEIT YDGVRITVEDVENTRIMMARLTKLEQEHVEEVPDADVVEAGEPTDNDVEPGDVTDSTVE BLAST Read more here: Source link

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The wheat stem rust resistance gene Sr43 encodes an unusual protein kinase

Mutant collection development We mutagenized 2,700 seeds of the wheat–Th. elongatum introgression line RWG34 containing Sr43 (ref. 29). Dry seeds were incubated for 16 h with 200 ml of a 0.8% (w/v) EMS solution with constant shaking on a Roller Mixer (Model SRT1, Stuart Scientific) to ensure maximum homogenous exposure of the…

Continue Reading The wheat stem rust resistance gene Sr43 encodes an unusual protein kinase

Splitting of VCF file of CSQ field in the INFO column to tabular format.

VCF file will be having seven fixed columns and INFO column. Chromosome, position, ID, ref, alt, qual, filter, and INFO column. This INFO column will be having the variant related information. In the INFO column CSQ field will be having multiple fields – 82 fields fixed with the delimeter “|”…

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An unusual tandem kinase fusion protein confers leaf rust resistance in wheat

Plant material Bread wheat accessions Transfer (TA5524), WL711, TA5605, Ae. umbellulata accession TA1851 and Ae. triuncialis accession TA10438 were obtained from the Wheat Genetics Resource Center (WGRC). TcLr9 (Transfer/6*Thatcher) is a near-isogenic line carrying Lr9 from Transfer in the genetic background of the susceptible wheat line Thatcher. TcLr9 and TA5605…

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how to change the format of file in R

how to change the format of file in R 0 I want to change the format of file from input to output (this is just an example of my data) input: > head(cpg_region2) cds downstream exon1 exons intron1 introns other promoter UTR3 UTR5 1 1_47963035 1_68276036 1_47963035 1_47963035 1_33831751 1_33831751…

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how to make a UpSet plot with data frame in R

how to make a UpSet plot with data frame in R 0 How to create a UpSet plot with my data, this is an example of data. I want to know how many of features are common between column names and how many are not overlap. for example, some features…

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Sample GenBank Record / Visual abstracts made easy with Mind the Graph

This page presents an annotated sample GenBank record (accession number U49845) in its GenBank Flat File format. You can check the corresponding alive record for U49845, and seeexamples of other records the show a range of biological features. SITE SCU49845 5028 bp DNA PLN 21-JUN-1999 DEFINITION Saccharomyces cerevisiae TCP1-beta gene,…

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ASM2874343v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::02/20/2023 15:33:27 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::6.4 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA Genes (total)::1,810 CDSs (total)::1,765 Genes (coding)::1,746 CDSs (with protein)::1,746 Genes (RNA)::45 rRNAs::3, 2, 2 (5S, 16S, 23S) complete rRNAs::3, 2, 2…

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Pinostrobin, a fingerroot compound, regulates miR-181b-5p and induces acute leukemic cell apoptosis

Leukemia cell culture The human acute promyelocytic leukemia cell line (NB4) and the human acute lymphocytic leukemia cell line (MOLT-4) were purchased from Cell Lines Service (Eppelheim, Germany). Leukemia cells were cultured in RPMI-1640 medium supplemented with 10% (v/v) FBS and 1% (v/v) penicillin–streptomycin (Gibco Life Technologies, Waltham, MA, USA)….

Continue Reading Pinostrobin, a fingerroot compound, regulates miR-181b-5p and induces acute leukemic cell apoptosis

how to make a venn plot with data frame in R

how to make a venn plot with data frame in R 0 I want to create a Venn plot with my data but this error occurred! ggvenn(venn_cpg_region2) Error in prepare_venn_data(data, columns, show_elements,show_percentage,:logical columns in data.frame data or vector columns should be length between 2 and 4 > head(venn_cpg_region2) cds downstream…

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Cumulative effects of weakly repressive regulatory regions in the 3’ UTR maintain PD-1 expression homeostasis in mammals

The PD-1 3’ UTR repressed reporter gene expression by promoting mRNA decay The human PD-1 3’ UTR is made up of 1,174 nucleotides, longer than its coding region (867 nts). To explore the revolutionary relationship of PD-1 3’ UTRs of species, we systematically analyzed the sequence conservation of 21,050 protein-coding…

Continue Reading Cumulative effects of weakly repressive regulatory regions in the 3’ UTR maintain PD-1 expression homeostasis in mammals

ASM2756334v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::05/23/2022 10:50:15 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::6.1 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::4,042 CDSs (total)::3,933 Genes (coding)::3,880 CDSs (with protein)::3,880 Genes (RNA)::109 rRNAs::11, 12, 9 (5S, 16S, 23S) complete rRNAs::6, 1, 1…

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Find data-based Gene_IDs for unknown gene_IDs in gtf.file

Find data-based Gene_IDs for unknown gene_IDs in gtf.file 0 Hi all, Following the RNA-seq analysis workflow, I am trying to find the GO gene ontology terms for a list of DGEs output of (FeatuCounts > edgeR). I conducted the RNA-seq analysis using either RAST-annotated gtf, or NCBI-PGAP gft files. 1…

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Circular mitochondrial-encoded mRNAs are a distinct subpopulation of mitochondrial mRNA in Trypanosoma brucei

Some mitochondrial mRNA are circularized CircTAIL-seq is a technique used to Illumina sequence individual transcript PCR libraries of mitochondrial mRNA tails. The approach captures enough of each molecule’s 5′ and 3′ termini that the presence of editing can be confirmed if necessary17. Library preparation first requires circularizing total RNA with…

Continue Reading Circular mitochondrial-encoded mRNAs are a distinct subpopulation of mitochondrial mRNA in Trypanosoma brucei

GENCODE – Mouse Release M32 Statistics

Statistics about the GENCODE Release M32 The statistics derive from the gtf file that contains only the annotation of the main chromosomes. For details about the calculation of these statistics please see the README_stats.txt file. General stats Total No of Genes 56953 Protein-coding genes 21565 – readthrough genes (not included)…

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ASM514463v2 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::03/20/2023 12:03:06 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::6.4 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA Genes (total)::9,670 CDSs (total)::9,591 Genes (coding)::9,573 CDSs (with protein)::9,573 Genes (RNA)::79 rRNAs::3, 5, 5 (5S, 16S, 23S) complete rRNAs::3, 5, 5…

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Discovery of two new isoforms of the human DUT gene

Overview of the isoform-specific determination of dUTPase gene expression Our aim was to determine the mRNA expression level of the dUTPase isoforms specifically. First, we investigated the Ensemble, the UniProt, and the NCBI Reference Sequences (RefSeq) databases and also took into account the Consensus CDS (CCDS) project. In the Ensemble…

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VEP/ CADD error – ERROR: Assembly is GRCh38 but CADD file does not contain GRCh38 in header.

Dear Biostars, I am having a confusing issue with my CADD plugin. This is confusing because when I run VEP for my whole trio – all the plugins work fine. However when I try to run CADD for individual – pivoted files – it no longer does and I get…

Continue Reading VEP/ CADD error – ERROR: Assembly is GRCh38 but CADD file does not contain GRCh38 in header.

Combination of whole genome sequencing and supervised machine learning provides unambiguous identification of eae-positive Shiga toxin-producing Escherichia coli

1. Introduction Shiga toxin-producing Escherichia coli (STEC) are important zoonotic pathogens comprising more than 400 serotypes (Beutin and Fach, 2015). Pathogenic STEC strains such as enterohemorrhagic E. coli (EHEC) may cause hemorrhagic colitis (HC) and hemolytic-uremic syndrome (HUS) in humans. However, it remains difficult to fully define human pathogenic STEC…

Continue Reading Combination of whole genome sequencing and supervised machine learning provides unambiguous identification of eae-positive Shiga toxin-producing Escherichia coli

ttc30a gene cDNA ORF clone, Xenopus tropicalis(tropical clawed frog)

The following ttc30a gene cDNA ORF clone sequences were retrieved from the NCBI Reference Sequence Database (RefSeq). These sequences represent the protein coding region of the ttc30a cDNA ORF which is encoded by the open reading frame (ORF) sequence. ORF sequences can be delivered in our standard vector, pcDNA3.1+/C-(K)DYK or…

Continue Reading ttc30a gene cDNA ORF clone, Xenopus tropicalis(tropical clawed frog)

Multimodal perturbation analyses of cyclin-dependent kinases reveal a network of synthetic lethalities associated with cell-cycle regulation and transcriptional regulation

Phylogenetic tree construction Tree diagram showing relationships between CDK proteins was constructed from a multi-sequence alignment (MSA) using Geneious95. The “Geneious Aligner”, was used to generate the MSA, and the neighbor joining method was used to construct the tree. All default parameters were used except where otherwise indicated. Combinatorial CRISPR…

Continue Reading Multimodal perturbation analyses of cyclin-dependent kinases reveal a network of synthetic lethalities associated with cell-cycle regulation and transcriptional regulation

Genetic immune escape landscape in primary and metastatic cancer

Inference of HLA-I tumor status with LILAC Inference of the correct HLA-I tumor status is fundamental to identifying GIE alterations (Fig. 1a), to estimate the neoepitope repertoire and burden and to predict the response to immune checkpoint inhibitors14,15 (ICIs). We have developed LILAC, a framework that performs HLA-I typing for…

Continue Reading Genetic immune escape landscape in primary and metastatic cancer

TTC30A gene cDNA ORF clone, Macaca mulatta(Rhesus monkey)

The following TTC30A gene cDNA ORF clone sequences were retrieved from the NCBI Reference Sequence Database (RefSeq). These sequences represent the protein coding region of the TTC30A cDNA ORF which is encoded by the open reading frame (ORF) sequence. ORF sequences can be delivered in our standard vector, pcDNA3.1+/C-(K)DYK or…

Continue Reading TTC30A gene cDNA ORF clone, Macaca mulatta(Rhesus monkey)

A draft human pangenome reference

Sample selection We identified parent–child trios from the 1KG in which the child cell line banked within the NHGRI Sample Repository for Human Genetic Research at the Coriell Institute for Medical Research was listed as having zero expansions and two or fewer passages, and rank-ordered representative individuals as follows. Loci…

Continue Reading A draft human pangenome reference

RefSeq: NC_015125 CDS #2356

RefSeq: NC_015125 CDS #2356 >NC_015125 (refseq) complement(2590281..2591861) /translation= MTASETRRYDVVIVGGGHNALVAAAYLARAGRSVVVLERSDAVGGAAVSERPWAGVDARV SRYSYLVSLLPPRIVDDLGLRIELRRRRYSSYTPDPADPSRGILIDTQDAEATAASFTRT LGDPDEAARYAAFGERLAPLGRAVFPTMTEPLPTEDEVRERVGDDELWSALTSRPLGDLL RSSFESDLVRGITLTDGLIGTFASSDDPSLAQNRCFLYHVIGGETGHWDVPVGGMGAVTA ELERVAREAGADIVTGVDVISVSPGGEVHGVTDRPEVFYGSLVLSGVGKAVLGRLLTAGG APTSVDEPEGAQVKVNMLLSRLPRLRDRSVSPEAAFAGTFHVNETMTQLDSGFVAATGGM LPDPLPLEIYCHSLTDPSILGEELRASGAQTLTLFGLQVPHRLLDDTDPVAAGARLLAAA QHSLDAVLDEPLRDCILRAPDGRLCIEARTTADLEESLNMVGGDIFHGGLSWPWLSAPAD TPAARWGVATGHARVLVCGSSAQRGGAVSGIGGQNAAMAALEILEG BLAST Read more here: Source link

Continue Reading RefSeq: NC_015125 CDS #2356

RefSeq: NC_015125 CDS #2849

RefSeq: NC_015125 CDS #2849 >NC_015125 (refseq) complement(3129850..3130794) /translation= MSASILPLHRPVGAARSARSTSSWRRVDRRLGVALLVPAFAVFAVFVFYPLGKVIWLSTQ GTDIFGQAAGFVGAKNFVTLFSDPHFGETLLRTAVFCVAVVAGRVVVGLAVTIPLTMTLR GMPIFRALLTSPLVVSVSAASVAFAAMLSPANGFVNSVITGFGGTAVPWLTSTQWAFPSV IAVTVWGSLGFTVLLLLGAFGAIDRDVIEAAHLDGAGPARTLWSISLPLVTPTLFFIVVT GAVEALTTFGQIQILTGGGPANSTSTLVYTIYTSAFGAGGANFGMAAATGIVLFVLVLGL SLVQFGLLEKRVNY BLAST Read more here: Source link

Continue Reading RefSeq: NC_015125 CDS #2849

RefSeq: NC_007795 CDS #975

RefSeq: NC_007795 CDS #975 >NC_007795 (refseq) 1028810..1032262 /translation= MKQIKKLLVANRGEIAIRIFRAAAELDISTVAIYSNEDKSSLHRYKADESYLVGSDLGPA ESYLNIERIIDVAKQANVDAIHPGYGFLSENEQFARRCAEEGIKFIGPHLEHLDMFGDKV KARTTAIKADLPVIPGTDGPIKSYELAKEFAEEAGFPLMIKATSGGGGKGMRIVREESEL EDAFHRAKSEAEKSFGNSEVYIERYIDNPKHIEVQVIGDEHGNIVHLFERDCSVQRRHQK VVEVAPSVGLSSTLRQRICDAAIQLMENIKYVNAGTVEFLVSGDEFFFIEVNPRVQVEHT ITEMVTGIDIVKTQILVAAGADLFGEEINMPQQKDITTLGYAIQCRITTEDPLNDFMPDT GTIIAYRSSGGFGVRLDAGDGFQGAEISPYYDSLLVKLSTHAISFKQAEEKMVRSLREMR IRGVKTNIPFLINVMKNKKFTSGDYTTKFIEETPELFDIQPSLDRGTKTLEYIGNVTING FPNVEKRPKPDYELASIPTVSSSKIASFSGTKQLLDEVGPKGVAEWVKKQDDVLLTDTTF RDAHQSLLATRVRTKDMINIASKTADVFKDGFSLEMWGGATFDVAYNFLKENPWERLERL RKAIPNVLFQMLLRASNAVGYKNYPDNVIHKFVQESAKAGIDVFRIFDSLNWVDQMKVAN EAVQEAGKISEGTICYTGDILNPERSNIYTLEYYVKLAKELEREGFHILAIKDMAGLLKP KAAYELIGELKSAVDLPIHLHTHDTSGNGLLTYKQAIDAGVDIIDTAVASMSGLTSQPSA NSLYYALNGFPRHLRTDIEGMESLSHYWSTVRTYYSDFESDIKSPNTEIYQHEMPGGQYS NLSQQAKSLGLGERFDEVKDMYRRVNFLFGDIVKVTPSSKVVGDMALYMVQNDLDEQSVI TDGYKLDFPESVVSFFKGEIGQPVNGFNKDLQAVILKGQEALTARPGEYLEPVDFEKVRE LLEEEQQGPVTEQDIISYVLYPKVYEQYIQTRNQYGNLSLLDTPTFFFGMRNGETVEIEI DKGKRLIIKLETISEPDENGNRTIYYAMNGQARRIYIKDENVHTNANVKPKADKSNPSHI GAQMPGSVTEVKVSVGETVKANQPLLITEAMKMETTIQAPFDGVIKQVTVNNGDTIATGD LLIEIEKATD BLAST Read more here: Source link

Continue Reading RefSeq: NC_007795 CDS #975

Bioinformatics Research Associate Job Opening in Nashville, TN at Vanderbilt University

The Bioinformatics Research Associate is part of the Creative Data Solutions (CDS) Shared Resource at Vanderbilt University and is a key individual contributor responsible for performing bioinformatics analyses of genomic data sets, developing and implementing (genetic and other) statistical models, and contributing to research studies. This position requires that the…

Continue Reading Bioinformatics Research Associate Job Opening in Nashville, TN at Vanderbilt University

Microorganisms | Free Full-Text | Whole Genome Sequencing of the Novel Probiotic Strain Lactiplantibacillus plantarum FCa3L

In this article, we present a description of the genome sequencing data and the draft genome of L. plantarum FCa3L. Genome sequencing was performed using the Illumina MiSeq platform and a total of 40 Mb raw data was obtained. The genome sequence of L. plantarum FCa3L at 30× coverage was…

Continue Reading Microorganisms | Free Full-Text | Whole Genome Sequencing of the Novel Probiotic Strain Lactiplantibacillus plantarum FCa3L

Roles of adenine methylation in the physiology of Lacticaseibacillus paracasei

Bacterial strains and cultivation Twenty-eight L. paracasei isolates (including L. paracasei Zhang) and a pglX gene-inactivated strain of L. paracasei Zhang were obtained from the Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, at the Inner Mongolia Agricultural University of China. For strain activation, the bacteria were cultivated…

Continue Reading Roles of adenine methylation in the physiology of Lacticaseibacillus paracasei

RefSeq: NC_001148 CDS #220

RefSeq: NC_001148 CDS #220 >NC_001148 (refseq) complement(join(437333..439427,439429..442742)) /translati MATPVRDETRNVIDDNISARIQSKVKTNDTVRQTPSSLRKVSIKDEQVKQYQRNLNRFKT ILNGLKAEEEKLSETDDIQMLAEKLLKLGETIDKVENRIVDLVEKIQLLETNENNNILHE HIDATGTYYLFDTLTSTNKRFYPKDCVFDYRTNNVENIPILLNNFKKFIKKYQFDDVFEN DIIEIDPRENEILCKIIKEGLGESLDIMNTNTTDIFRIIDGLKNKYRSLHGRDVRIRAWE KVLVDTTCRNSALLMNKLQKLVLMEKWIFSKCCQDCPNLKDYLQEAIMGTLHESLRNSVK QRLYNIPHNVGINHEEFLINTVIETVIDLSPIADDQIENSCMYCKSVFHCSINCKKKPNR ELRPDSTNFSKTYYLQGAQRQQQLKSSAKEQKSWNKTQKKSNKVYNSKKLVIIDTGSGVN ITNDKTLLHNYEDSNRSTRFFGIGKNSSVSVKGYGYIKIKNGHNNTDNKCLLTYYVPEEE STIISCYDLAKKTKMVLSRKYTRLGNKIIKIKTKIVNGVIHVKMNELIERPSDDSKINAI KPTSSPGFKLNKRSITLEDAHKRMGHTGIQQIENSIKHNHYEESLDLIKEPNEFWCQTCK ISKATKRNHYTGSMNNHSTDHEPGSSWCMDIFGPVSSSNADTKRYMLIMVDNNTRYCMTS THFNKNAETILAQIRKNIQYVETQFDRKVREINSDRGTEFTNDQIEEYFISKGIHHILTS TQDHAANGRAERYIRTIVTDATTLLRQSNLRVKFWEYAVTSATNIRNCLEHKSTGKLPLK AISRQPVTVRLMSFLPFGEKGIIWNHNHKKLKPSGLPSIILCKDPNSYGYKFFIPSKNKI VTSDNYTIPNYTMDGRVRNTQNIYKSHQFSSHNDNEEDQIETVTNLCEALENYEDDNKPI TRLEDLFTEEELSQIDSNAKYPSPSNNLEGDLDYVFSDVEESGDYDVESELSTTNTSIST DKNKILSNKDFNSELASTEISISEIDKKGLINTSHIDEDKYDEKVHRIPSIIQEKLVGSK NTIKINDENRISDRIRSKNIGSILNTGLSRCVDITDESITNKDESMHNAKPELIQEQFNK TNHETSFPKEGSIGTKCKIPKYRQWISLKTGDTSLPIKTLESINNHHSNDYSTNKVEKFE KENHHPPPIEDIVDMSDQTDMESNCQDGNNLKELKVTDKNVPTDNGTNVSPRLEQNIEAS GSPVQTVNKSAFLNKEFSSLNMKRKRKRHDKNNSLTSYELERDKKRSKRNRVKLIPDNME TVSAQKIRAIYYNEAISKNPDLKEKHEYKQAYHKELQNLKDMKVFDVDVKYSRSEIPDNL IVPTNTIFTKKRNGIYKARIVCRGDTQSPDTYSVITTESLNHNHIKIFLMIANNRNMFMK TLDINHAFLYAKLEEEIYIPHPHDRRCVVKLNKALYGLKQSPKEWNDHLRQYLNGIGLKD NSYTPGLYQTEDKNLMIAVYVDDCVIAASNEQRLDEFINKLKSNFELKITGTLIDDVLDT DILGMDLVYNKRLGTIDLTLKSFINRMDKKYNEELKKIRKSSIPHMSTYKIDPKKDVLQM SEEEFRQGVLKLQQLLGELNYVRHKCRYDINFAVKKVARLVNYPHERVFYMIYKIIQYLV RYKDIGIHYDRDCNKDKKVIAITDASVGSEYDAQSRIGVILWYGMNIFNVYSNKSTNRCV SSTEAELHAIYEGYADSETLKVTLKELGEGDNNDIVMITDSKPAIQGLNRSYQQPKEKFT WIKTEIIKEKIKEKSIKLLKITGKGNIADLLTKPVSASDFKRFIQVLKNKITSQDILAST DY BLAST Read more here: Source link

Continue Reading RefSeq: NC_001148 CDS #220

ASM393416v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::12/27/2018 19:23:50 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.7 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::5,099 CDSs (total)::5,045 Genes (coding)::4,882 CDSs (with protein)::4,882 Genes (RNA)::54 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1 (5S,…

Continue Reading ASM393416v1 – Genome – Assembly

RefSeq: NC_023151 CDS #1082

RefSeq: NC_023151 CDS #1082 >NC_023151 (refseq) complement(1122011..1123042) /translation= MKNLLDLSYEELVTEITNLGLERYRADQILDWVFDKKVNNFDEMTNLSKKHRALLKEHFS ISFLKLLDKKVSRIDGTTKFLWELEDGNTIESVMLFHPDRITACISTQVGCPVKCIFCAT GMSGFVRNLTTGEIVAQILSMEKEEKKKIGNVVYMGMGEPLLNYENTIKSIRILNHKKMG NIGIRRITISTVGIPDRIIQLAEEGLDVKLALSLHAPTNFKRDQLVPLNKKYSIEEILNA VKIYQRKTGNRVTIEYVLIRGINDEISDAKKLAEILRNMKVFVNLIPVNPTVEGLRRPSR ERLLTFKRILLENGIEAEIRREKGTDIEAACGQLRLKRIKSRS BLAST Read more here: Source link

Continue Reading RefSeq: NC_023151 CDS #1082

RefSeq: NC_023151 CDS #489

RefSeq: NC_023151 CDS #489 >NC_023151 (refseq) complement(487497..488600) /translation= MGLKAHAMVLEKFNQPLVYKEFEISDIPRGSILVEILSAGVCGSDVHMFRGEDPRVPLPI ILGHEGAGRVVEVNGEKRDLNGELLKPGDLIVWNRGITCGECYWCKVSKEPYLCPNRKVY GINRGCSEYPHLRGCYSSHIVLDPETDVLKVSEKDDLDVLAMAMCSGATAYHAFDEYPES FAGKTVVIQGAGPLGLFGVVIARSLGAENVIVIAGSPNRLKLAEEIGADLTLNRRETSVE ERRKAIMDITHGRGADFILEATGDSRALLEGSELLRRGGFYSVAGVAVPQDPVPFKVYEW LVLKNATFKGIWVSDTSHFVKTVSITSRNYQLLSKLITHRLPLKEANKALELMESREALK VILYPEG BLAST Read more here: Source link

Continue Reading RefSeq: NC_023151 CDS #489

Detection of Burkholderia pseudomallei with CRISPR-Cas12a based on specific sequence tags

1. Introduction Melioidosis is a tropical disease caused by the aerobic, Gram-negative motile bacillus which is classified as a category B biological agent by the Centers for Disease Control and Prevention (CDC) of America (1, 2). It is a highly pathogenic endemic zoonotic disease in many tropical countries, particularly in…

Continue Reading Detection of Burkholderia pseudomallei with CRISPR-Cas12a based on specific sequence tags

Adding ‘gene_name’ attribute to each row of GTF/GFF file (missing for CDS, transcript, and exon rows)

Hello, Can someone please help me with this issue I’m having? Thank you in advance! I have a GFF file, and I have the gene_name attribute in my GFF file, but it’s only present for each gene entry (i.e., it’s absent from the transcript, cds, and exon rows). I want…

Continue Reading Adding ‘gene_name’ attribute to each row of GTF/GFF file (missing for CDS, transcript, and exon rows)

4. A GenBank-formatted DNA sequence file is presented

Transcribed image text: 4. A GenBank-formatted DNA sequence file is presented below. Assume that this sequence represents the sense strand, starts with the 5’UTR, contains two exons, has a single intron, and ends with the 3 ‘UTR. The protein coding sequences have the following coordinates: 343..561,760..1353 (indicated at the CDS…

Continue Reading 4. A GenBank-formatted DNA sequence file is presented

A high-quality chromosomal-level genome assembly of Greater Scaup (Aythya marila)

Ethics statement All animal experimental procedures were approved by the Biomedical Ethics Committee of Qufu Normal University (approval number: 2022001). Sampling and sequening The experimental sample is a wounded male duck found during the wild bird survey in Jiangsu, China, which died unexpectedly during rescue. We dissected the sample and…

Continue Reading A high-quality chromosomal-level genome assembly of Greater Scaup (Aythya marila)

desgin a primer for CDS

desgin a primer for CDS 0 I want to desgin a primer for the mRNA, now I have some cell samples, it contains gDNA, mRNA(not only the target gene) More detail: I need to use the pcr to amplyfy the target gene mRNA(mature), now I need to design a primer…

Continue Reading desgin a primer for CDS

Broad Institute of MIT and Harvard hiring Senior Software Engineer, Bioinformatics in Cambridge, Massachusetts, United States

Job DescriptionThe Cancer Data Science (CDS) team at the Broad (www.cancerdatascience.org/) is an interdisciplinary group dedicated to accelerating cancer research. We help design and analyze large-scale experiments, develop new statistical tools and machine learning methods, write papers, produce datasets used by tens of thousands of researchers around the world, and…

Continue Reading Broad Institute of MIT and Harvard hiring Senior Software Engineer, Bioinformatics in Cambridge, Massachusetts, United States

Annotate CDS and UTR given transcript

Annotate CDS and UTR given transcript 1 I am annotating a new genome and I am combining several sources of information for the annotation. It combines a de novo annotation as well as lifting over annotations from closely related species. I have been using GFFCompare (ccb.jhu.edu/software/stringtie/gffcompare.shtml) to merge GFF files….

Continue Reading Annotate CDS and UTR given transcript

Phenotypic and Genetic Analysis of KPC-49

Introduction The worldwide dissemination of carbapenem-resistant Enterobacteriaceae (CRE), particularly carbapenem-resistant K. pneumoniae (CRKP), poses a significant risk to public health. CRKP can cause various infections, such as urinary tract infections, bloodstream infections, and pneumonia, leading to high morbidity and mortality.1 Prevention and control of K. pneumoniae infection are becoming more…

Continue Reading Phenotypic and Genetic Analysis of KPC-49

RefSeq: NC_007481 CDS #1518

RefSeq: NC_007481 CDS #1518 >NC_007481 (refseq) 1677437..1678456 /translation= MLSVSQLSIDYGSNRVVSDLNLSLGNNEILMLVGPTGCGKSTILQALAGLIPISEGEINS GKWRATPKITVPAEKRSVGMVFQDFALFPHLTVQQNIFFRLKDTSPGEHWIKLLGLDEFR NKKPATLSGGQKQRVALARTLAHQPDFVLLDEPLSNLDAALKDMLRWDIRNALKAAGVPA IWVTHDQEEALSVGDRVGVLQGGKIQQIDTPERCFSMPNNRFVARFLGEASFISGQFSQG QATTSIGNAPAHGVDCESGDVDVLLRPDDVLLVQSSVGNNGEIIWVRFEGGSRLCAIKLA CGTVVTSRVSHEIVVNPGDAVHVSLSTSHPLAVYKQLAQ BLAST Read more here: Source link

Continue Reading RefSeq: NC_007481 CDS #1518

rna seq – Why is there antisense sequence in RNAseq data

I’m looking at RNAseq data from CCLE. The data is paired-end. Take the cell line Hs578T and the gene HRAS as an example. The cell line carries a G12D mutation (c.35G>A), so the change in cds is: ggc ggtgtgggca agagtgcgct g – Wildtype CDS gAc ggtgtgggca agagtgcgct g – Mutant…

Continue Reading rna seq – Why is there antisense sequence in RNAseq data

RefSeq: NC_013722 CDS #1522

RefSeq: NC_013722 CDS #1522 >NC_013722 (refseq) complement(1852142..1854817) /translation= MMESLPPKQSGTRSFVFAEGAQWVRADFHLHTRADREFKYTGDDNFYNSNYVDALENAGI RLGVITNHNKFDFDEFKALRKTAQKKGIALLPGVELSVNDGANGIHTLVVFSDDWLADGH DHINPFLGVSFKGKVPAQYEQENGRSSLSLVNTIEELESYHRDFFLVFAHVEAPSGLWAE LDGGRLAELGRNELFRRRTLGFQKVRTYNKVQEKNKPCRTKAQQHLGDWYPAELEGCDAK CIEDIGQGKACYLKLGELSFEAVKFALSDPAARVATEPPKHQASHIRRIHFDGGILDGQT LHFSSELNTLIGIRGSGKSSILEAVRYALDIPRGEKAQDTKYKDELIRHTLGSGGKVTLT ACDVYGQEFTISRIFREAPNVYLGGKLQPGVSIRETVLRRPIYFGQKDLSSTGEGFETDL VEKLVGEKLRVLRDEIEVQRQRVRDAAQRWLKLSNTAELKRDFETQLNDANFRLTKFAEH GVADKLQKRLGFQQDATALARMMERADSFILALGSLIAEHEDELRNATSYVSKQNPDFFT AYYAEFSNLVAKVDQLKQIEREANVIAARLKTKQGEFEGASRSLQEEFAQVERQLAQELK QTGMTAIQPDDFLAQQQRKTKAEQMLQALTKQESQQTSIRDALFAEIDKLNELWLSEFNT IKAELDRVNAGHTALQIKADFKGDKEAAISFMQQLFKGSNIRETTLRAAMEDYADFGGLL RALPSALAKAGSTPEIFEKTFMQNLTEFVIWQVPNHFVIGYHGKELKHHSLGQRASALLL YVLSQRQNDVIIIDQPEDDLDNQTIYDDVIKLLCQMKPHAQFIFATHNANFPVLGGAEQV HACRYQDEKVAVQSGSIDARPVQDAIINIMEGGQEAFNRRKEVYNLWKPQS BLAST Read more here: Source link

Continue Reading RefSeq: NC_013722 CDS #1522

RefSeq: NC_018080 CDS #1594

RefSeq: NC_018080 CDS #1594 >NC_018080 (refseq) 1718490..1722836 /translation= MPISSSSARRAEPAPRPLAEFHPAVRQWFERHFAAPTPAQVEAWPAIREGLSTLVAAPTG SGKTLTAFLAAIDALVVEGLAAGGELADATQVVYVSPLKALSNDIRINLEQPLAGIREEL ARLGLPDVDIRSAVRTGDTPQVERGAMRKRPPHILVTTPESLYILLGSESGRQMLAGVRS VIVDEIHALAGSKRGSHLALSLERLQALCPRPLLRIGLSATQKPIEKVARFLVGASGNPR DPACRIVDIGYTRPRDLGIEVPPVALEAVMSNDTWELVYDRLAHLAGEHRTTLVFVNTRR MAERVTRFLAERLGSRQVAAHHGSLAKELRLDAEQRLKAGQLKVLVATASLELGIDIGDV ELVCQLSSPRSIAAFLQRVGRSGHSVGGTPKGRLFPTSRDDLVECAALLDSVRRGELDSL VLPRQPLDVLAQQIVAEVACQEWREDDLYRLVIRAEPYAGLERERFDEVLRMLAEGYHSR LGVRGAYLHRDALNGLLRGRRGARLTALTSGGTIPDTGDYSVLLEPQGLLVGTVNEDFAV ESLAGDVFQLGNTSYRIIRIEPGRVRVEDAQGQPPNIPFWLGEAPGRSDELSASVARLRD TLDELLGEGQALPEGQRLEPAIAWLGATLGLDDGAARQIVEYLARARQALGGLPGSRRLV MERFFDESGGMQLIIHSPHGSRLNRAWGLALRKRFCRSFNFELQAAATEDAIILSLSTSH SFPLDEVWRYLHSASAEHLLVQAVLDAPLFGVRWRWNLTTSLGLPRYAGGRKVPPQLLRM KSEDLLASVFPDQVACLENIVGEREVPDHPLVAQTLDDCLHEAMDCEGWLALLRDMESGA VDLLARDLPAPSALAAEILTARPYAYLDDAPLEERRTQAVQNRRWSDPESADDLGALDLE AIEAVRGEAWPEARNADEMHEALNSLGFLTSGEAEANPGWGEWLAQLSEQRRAGRLDCAG STLWLAAERLPAMRLVHPAAKVPDAFQAPRGYPPPDSAEAATVELTRARLGGFGPRTAGQ LAADLGIGLADQQYALAALEREGYVLRGRFSPGATEEEWCERHLLARIHRYTVKRLRREI EPVERADFMRFLFDWQRLAPGTRGRGAESLATVVEQLEGFQAAAAAWESELLAARVADYA SHWLDQLCRSGRIVWARLAGRSKAAGGPLRSAPIVLLPRRELGLWSVLQRDAPEPELSPR AARVLEVLREQGASFFDELSQDAHLLRSELENALGELVSVGRVNADSFAGLRTLLMPADK RSRQERRSRGLPGGMQDAGRWAPLRRAKVEEAGQRLPAEVLEHVARTLLRRYGVVAWRLL EREADWLAPWRELLRVYHRLEARGEIRGGRFIAGLAGEQFALAEAVGLLREVRKRPPDGA MLVVSAVDPLNLVGGLLPGERVPAVTGNRLLYRDGAPLAALVAGKVRMLAEDDGETAQQI RALLIRRH BLAST Read more here: Source link

Continue Reading RefSeq: NC_018080 CDS #1594

Craig Venter Has Mixed Feelings On DNA Day Celebrations

The International Human Genome Sequencing Consortium announces the completion of a “working draft” … [+] human genome sequence. Craig Venter (left, Celera Genomics), President Bill Clinton (center), and Francis Collins (right, NHGRI) at the White House Press Conference regarding the completion of the working draft of the human genome. NIH…

Continue Reading Craig Venter Has Mixed Feelings On DNA Day Celebrations

RefSeq: NC_003281 CDS #295

RefSeq: NC_003281 CDS #295 >NC_003281 (refseq) complement(join(1125565..1125682,1125810..1125896, /transl MQYLQFLSLVVLLLMCHARKSVYRRNSPSLRRLTRNYDWEVDEHGGLKPIINPAKVERAT KNCANDSFILGTIMSNYNRHKIPGGQVDVEVEVWVQEITTISDITSDFQLDIYIYETWYD PALNYAFMNPCKYNLSLNSVLLEKLWTPNSCFINSKTADIHKSPFPNIFLMIYANGTVWT NYRLKLQGPCIMDLTKFPFDNVTCSLTFESFNYNTDEVKMDWSVNGVQKMRDKMELADYE LVDIHKIRTTEEYPAGYWHELTMSFEFKRRAGWYILQAYLPTYLTICISWISFALGSKAI PARTMLGVNSLLAMTFQFGNIIRNLPRVSYVKAIDVWMLSCMTFVFCSLLELAWVGYLSR EEEPTSAKCLQPSAQVAPKPCHPPPVQQNANNSSVHRRQKQPKNEEESALLSLRDNDYGY IPPGFGLNGNVANAMKSFSSSCSCEPTNVVNLMLDEAETIPTSTSSSLSRKQRREILAHK IDSVSVFMFPFLFVLFNIAYWQHYLRGY BLAST Read more here: Source link

Continue Reading RefSeq: NC_003281 CDS #295

Extract CDS reads from a BAM file

Extract CDS reads from a BAM file 1 Hi everyone, I am looking for a way to extract the sequences of the reads that map to the CDS of my reference. I used samtools -b -L CDS.bed BAM.bam > BAM_CDS.bam. That allowed me to get all the reads that overlap…

Continue Reading Extract CDS reads from a BAM file

RefSeq: NC_012490 CDS #2240

RefSeq: NC_012490 CDS #2240 >NC_012490 (refseq) complement(2447222..2448220) /translation= MKGSGIKAEIPVPDTGSNIGKMAVVVFSWVASFGGLVVNPSNTWTAFNNSGGGNSSVNLA VYYRRLTGNDATIAFTGMQSQPWTATMYIFDNANPPQTRDPEFRSTTNVADCPMNSDFAT IEGSYTVAHVVTRGIAGWTGATAGMFFSETSGTGTAGMSAGEAHFPEREFGRVADGQRFT KVANGTATAFTFTVGVMVATNGLEKSERKFPANAAVEAPMTAGPTPLWVDFNAYQHSSGP DYGNANGFVLPAAGYGAIMLTATRKWWGYQPWVSLLFNGIVYKEVQAETISPWTPITIPE GMTVTARGAVVGSNASADDRTFNGSTLTLLTV BLAST Read more here: Source link

Continue Reading RefSeq: NC_012490 CDS #2240

RefSeq: NC_019776 CDS #2091

RefSeq: NC_019776 CDS #2091 >NC_019776 (refseq) complement(2538015..2539823) /translation= MALIVQKYGGSSVGSTDRIKSVSKRIYKTVQEGNQVVVVVSAMGKTTDGLVKLAHEITSN PCRREMDMLLSTGEQVSISLLSMALQEIGQSAISLTGAQVGISTEANYSKARILEIKTDR INRHLEQGQVVVVAGFQGIIHGEELEITTLGRGGSDTSAVALAVALQADCCEIYTDVPGI LTTDPRIVPSAKLMDEITADEMLELASLGAKVLHPRAVEIARNFGMPLVVKSSWTDDPGT RVISPPNQGKSLVGLEITKAVDAVQYDADQAKVALLRVPDRPGVAARLFGEIARHDVDVD LIIQSIHEGNSNDIAFSVVKGVLPKAEAVAMAIAPILGDSGNTDILVEKKIAKIAIAGAG MIGRPGIAAQMFQALAKAKVNIQMISTSEVKVSCIVAEDECDRAIAALCETFNIASSSVT LNDNSKDIANLVPVRGVALDQNQAQLAILFVPDVPGMAAKIFTVLADANISVDMIIQSQR CRLVDGIPMRDIAFTVAQSDAEEAKKALYQLQSEIKFKEIVVEPHIAKVSIVGSGMIGSP GVAAKFFSALAQEKINISMITTSEIKISCVVDESQAIQALKAVHEAFGLGGETLLEVPSK EG BLAST Read more here: Source link

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Stream R-Studio 8.3 Build 168003 Network Edition PORTABLE Crack – PORTABLE Crackingpatc .rar by Carrie Harris

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Quantitative Synthetic Biology for Biologics Production

Biologics accounted for more new drug approvals than did small molecules for the first time in 2022, marking a significant shift in the pharmaceutical industry (1). Large-molecule pipelines are also moving from standard monoclonal antibodies (MAbs) to more complex and difficult-to-express molecules, which intensifies pressure on the industry to meet…

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RefSeq: NC_009719 CDS #1456

RefSeq: NC_009719 CDS #1456 >NC_009719 (refseq) 1573431..1574933 /translation= MAKDLTHFIGGKHVAGTSGRFLDVTNPNTGEVTARTPLASAAELRAAVSVAAKAFPEWAA TNPQRRARVMFEFKRLLEANMNELAELLSAEHGKVIADSKGDVQRGLEVIEFACGIPHLM KGEFTEGAGPGIDMYSMRQPLGVCAGITPFNFPAMIPMWMFGVSIACGNTFIVKPSEKDP SVPIRLAELFMEAGAPAGVLNVVNGDKEAVDAILTDPMIQAVSFVGSSDIAQYVYATGTA HGKRVQAMGGAKNHAIIMPDADMDQVVNDLIGAGYGSAGERCMAISVAVPVGEDTADRLV EKLVPRVQSLKVGISTAADSDYGPLVTKAHMDKVSSYIEMGVKEGAKLLVDGRGFKLQGY ENGFFLGGSLFDHVTPDMQSYKDEIFGPVLQIVRAKTFDEAAELPTNHQYGNGVAIFTRD GDAARSFASRVQVGMVGINVPIPVPLAYHTFGGWKRSAFGDTNQHGTEGVKFWTHIKTVT SRWPTGGVKEASSFVIPTMK BLAST Read more here: Source link

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RefSeq: NC_000913 CDS #341

RefSeq: NC_000913 CDS #341 >NC_000913 (refseq) 368611..370275 /translation= MAIQHPDIQPAVNHSVQVAIAGAGPVGLMMANYLGQMGIDVLVVEKLDKLIDYPRAIGID DEALRTMQSVGLVDDVLPHTTPWHAMRFLTPKGRCFADIQPMTDEFGWPRRNAFIQPQVD AVMLEGVSRFPNVRCLFSRELEAFSQQDDEVTLHLKTAEGQREIVKAQWLVACDGGASFV RRTLNVPFEGKTAPNQWIVVDIANDPLSTPHIYLCCDPVRPYVSAALPHAVRRFEFMVMP GETEEQLREPQNMRKLLSKVLPNPDNVELIRQRVYTHNARLAQRFRIDRVLLAGDAAHIM PVWQGQGYNSGMRDAFNLAWKLALVIQGKARDALLDTYQQERRDHAKAMIDLSVTAGNVL APPKRWQGTLRDGVSWLLNYLPPVKRYFLEMRFKPMPQYYGGALMREGEAKHSPVGKMFI QPKVTLENGDVTLLDNAIGANFAVIGWGCNPLWGMSDEQIQQWRALGTRFIQVVPEVQIH TAQDNHDGVLRVGDTQGRLRSWFAQHNASLVVMRPDRFVAATAIPQTLGKTLNKLASVMT LTRPDADVSVEKVA BLAST Read more here: Source link

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RefSeq: NC_020832 CDS #765

RefSeq: NC_020832 CDS #765 >NC_020832 (refseq) 802346..803437 /translation= MEEKEILWNEAKAFIAACYQELGKEEEVKDRLEDIKSEIDLTGSYVHTKEELEHGAKMAW RNSNRCIGRLFWNSLNVIDRRDVRTKEEVRDALFHHIETATNNGKIRPTITIFPPEEKGE KQVEIWNHQLIRYAGYESDGERIGDPASCSLTAACEELGWRGERTDFDLLPLIFRMKGDK QPVWYELPRSLVIEVPITHPDIEAFSDLELKWYGVPIISDMKLEVGGIHYNAAPFNGWYM GTEIGARNLADEKRYDKLKKVASVIGIAADYNTDLWKDQALVELNKAVLYSYKKQGVSIV DHHTAASQFKRFEEQEEEAGRKLTGDWTWLIPPISPAATHIFHRSYDNSIVKPNYFYQDK PYE BLAST Read more here: Source link

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Diversity | Free Full-Text | Phylogenomic Analysis of Two Species of Parasenecio and Comparative Analysis within Tribe Senecioneae (Asteraceae)

Received: 6 December 2022 / Revised: 9 April 2023 / Accepted: 11 April 2023 / Published: 17 April 2023 Round 1 Reviewer 1 Report This article present Phylogenomic Analysis of Two Species of Parasenecio and Comparative Analysis Within Tribe Senecioneae (Asteraceae). Before recommending this article for publication, there are some…

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ASM145693v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::11/20/2015 18:41:21 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::3.0 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes::4,429 CDS::4,289 Pseudo Genes::51 rRNAs::7, 6, 6 (5S, 16S, 23S) complete rRNAs::7 (5S) partial rRNAs::6, 6 (16S, 23S) tRNAs::70 ncRNAs::0 ##Genome-Annotation-Data-END## Read…

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ASM2582178v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::08/12/2020 16:04:36 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.12 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::6,023 CDSs (total)::5,968 Genes (coding)::5,473 CDSs (with protein)::5,473 Genes (RNA)::55 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1…

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ASM2139437v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::01/04/2022 11:23:08 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.3 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::4,440 CDSs (total)::4,351 Genes (coding)::4,331 CDSs (with protein)::4,331 Genes (RNA)::89 rRNAs::6, 7, 2 (5S, 16S, 23S) complete rRNAs::6, 7, 2…

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gff to gtf missing gene id

gff to gtf missing gene id 1 Hi, I was trying my hand at annotating a genome using prokka, and I’ve converted the output gff file to gtf (gffread file.gff -T -o file.gtf) and this is what my gtf file looks like: CP001095.1 prokka transcript 210 1712 . + ….

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ASM2462300v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::08/05/2022 11:08:20 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::6.2 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::6,035 CDSs (total)::5,966 Genes (coding)::5,796 CDSs (with protein)::5,796 Genes (RNA)::69 rRNAs::1, 3, 6 (5S, 16S, 23S) complete rRNAs::1 (5S) partial…

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Error using BWA to map environmental transcriptome against a genomic reference

I have quality controlled paired end environmental transcriptomic data that I want to map against a reference database of 8 cyanobacterial genomes. I made this reference by joining together the fasta files of each genome. I performed this mapping with BWA v0.7.3a but noticed that when I tried to count…

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data file link: | Chegg.com

data file link: drive.google.com/file/d/1Odr12yDiUwI02-BfaXrHehKBM1uMW_1N/view?usp=share_link Step 1 (5pts) Load the file GSE124548.raw.txt into R and create a new dataframe with just the columns with the raw counts for healthy (HC) and CF patients before treatment (Base) and call it readcount. Use the first column (EntrezID) in the original file as the…

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RefSeq: NC_000964 CDS #917

RefSeq: NC_000964 CDS #917 >NC_000964 (refseq) 975231..976409 /translation= MSQNDSGHFLISEENWSLHRKGFDDQQRHQKKVQEAIKNNLPDLVTEESIIMSNGKDVVK IPIRSLDEYKIRYNYDKNKHVGQGDGESQVGDVVARDGSDKKQGPGKGQGAGDQAGEDYY EAEVSLMDLEEALFKELELPNLQQKERDNIIHTDIEFNDIRKTGLTGNIDKKRTMMSAFK RNAMSGKPSFYPIYPEDLKYKTWNDITKPESKAVVLAMMDTSGSMGVWEKYMARSFFFWM TRFLRTKYETVEIEFIAHHTEARVVSEEDFFSKGESGGTICSSVYRKSLELIDEKYNPAR YNIYPFHFSDGDNLTSDNARCVKLVNDIMKKANLFCYGEVNQYNRHSTLMSAYKNVKDEK FKYYILKQKSDVFQALKNFFRNEESGVSHQFS BLAST Read more here: Source link

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Maker Gff3 file issues

Maker Gff3 file issues 1 Hi community, This is really a technical question, I hope it is OK to post it here… I am trying to import the gff3 file from Maker to my Jbrowse to view the annotations. I am using the maker2jbrowse script and getting constant errors. There…

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Antismash on Fasta files

Hello, you can provide FASTA files to it ########### antiSMASH 6.1.1 ############# usage: antismash [–taxon {bacteria,fungi}] [–output-dir OUTPUT_DIR] [–output-basename OUTPUT_BASENAME] [–reuse-results PATH] [–limit LIMIT] [–minlength MINLENGTH] [–start START] [–end END] [–databases PATH] [–write-config-file PATH] [–without-fimo] [–executable-paths EXECUTABLE=PATH,EXECUTABLE2=PATH2,…] [–allow-long-headers] [-v] [-d] [–logfile PATH] [–list-plugins] [–check-prereqs] [–limit-to-record RECORD_ID] [-V] [–profiling] [–skip-sanitisation] [–skip-zip-file]…

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GFF/GTF file error / featureCounts

Hi all, I am trying to generate a count.matrix for sorted bam files, using featureCounts on linux. I have a non-modal organism (bacteria), so I generated the annotation.file using both PROKKA and RAST. I used all the following files in featurecounts; PROKKA.gff, RAST.gff RAST.gtf gffread converted-PROKKA.gtf file But still facing…

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Phylogenomic analysis uncovers a 9-year variation of Uganda influenza type-A strains from the WHO-recommended vaccines and other Africa strains

Demographic characteristics of sampled patients The Uganda Virus Research Institute National Influenza Centre (UVRI-NIC) laboratory tested 18,353 patients between 22nd October 2010 and 9th May 2018. Thirteen-percent (2404/18,353) were positive for influenza, 69.88% (1680/2404), 29.62% (712/2404), and 0.17% (4/2404) had influenza A, B, and A/B co-infection, respectively (Fig. 1A). IAV positives…

Continue Reading Phylogenomic analysis uncovers a 9-year variation of Uganda influenza type-A strains from the WHO-recommended vaccines and other Africa strains

Extract genes within a genome using eUtils

Extract genes within a genome using eUtils 0 Hi, I have a bunch of EC numbers based on which I would like to download the corresponding genes from several species. An example of a search would be “Bacillus[ORGN] AND 1.7.7.2[EC/RN Number]” and if I use: esearch -db nuccore -query “Bacillus[ORGN]…

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