Tag: CDS

RefSeq: NC_016109 CDS #7550

RefSeq: NC_016109 CDS #7550 >NC_016109 (refseq) 8714945..8716276 /translation= MPAPAPCPPAPGQVPLLGHAPALLRRPLSFFEATRTAEPLVRVGFGPIRLYLANDPALVH RIQVDTDSFERGRFFERLASNFGNPLIASDGAEHQHQRRALKPAFSRRSVRDHTSAITEE TERRIGAWRPGTVVAADEEMSDLVAAVVLRSLFSTRLSPTTVRDIRETLFLIARRLLVRT VFPDIVSSLPTPGNRRFAASVGRFHTTVDELIRERRANPRPHHDILQTLLTTRHPATGAP LSDTEIRSEFLMLLFAALETTSTSLSWAVFEVARRPDVQHRLQNEADTVTAGGPLGYDRL KNLTYTRQVIDETLRLHAPMLFTRRARHDVTLAGITVPAGSEVGYSPRAVHRDPGLYPHP AAFDPDRTAPDSATDRPQGAYFPFGTGPHRCIGEHLALTTMTTALATLATKWNLRIAPGT RIRETNSSLPHLSSLPLLPTPRG BLAST Read more here: Source link

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Mapping RNA-Seq reads onto viral genome

Mapping RNA-Seq reads onto viral genome 0 Hi everyone, I have 6 files of paired-end 75 nt RNA-Seq reads from HEK293 I want to map onto the AAV genome. I got the reference genome as a fasta file and the annotation file as gff3/gtf from NCBI. For mapping onto the…

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openapi – Is there a way using swagger to auto generate the error responses for APIs developed using SAP CAP

I have included cds-swagger-ui-express within my application to auto-generate the openAPI documentation as well as host it from the server itself. I was looking for a way to auto-generate the error response documentation by swagger itself. Below is my code with the existing document that is generated // srv/todo-service.js const…

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RefSeq: NC_018296 CDS #388

RefSeq: NC_018296 CDS #388 >NC_018296 (refseq) complement(913115..916258) /translation= MATRHSVSHITSSGEPETPQERQKRFLLEVDAKHAYANDKDDATKRFQYLLGLSAIFRKF IDLNASKDPEFKKRVREIDSKSLFKESTKKKKKSNSRRRKTEKEEDAELLQDEEHQDDEE NQHTVFTESPSYIKEGTLREYQIQGLNWLISLYENRLSGILADEMGLGKTLQTISFLGYL RYVKNIDGPFIIIVPKSTLDNWRREFAKWTPDVSVVVLQGDKESRANIIKDRLYTADFDV LITSFEMVLREKSALKKFKWEYIVVDEAHRIKNEQSSLSQIIRLFYSRNRLLITGTPLQN NLHELWALLNFLLPDVFGDSEQFDDTFDQQNNNEQDKKTKAEEQDKVIQELHQLLSPFLL RRVKSDVEKSLLPKIETNVYTGMTDMQVSWYKNLLEKDIDAVNGVVGKREGKTRLLNIVM QLRKCCNHPYLFDGAEPGPPYTTDEHLVYNSGKMIILDKMLKKFKQEGSRVLIFSQMSRV LDILEDYCYFREYEYCRIDGSTAHEDRIEAIDEYNAPDSDKFIFLLTTRAGGLGINLTSA DVVILYDSDWNPQADLQAMDRAHRIGQKKQVKVYRFVTENAIEEKVLERAAQKLRLDQLV IQQGRQANAGTNVGSSKDDLIEMIQHGAQKVFEESKSTVVDDDIESILARGAEKTKTMNE KFNKLGLEDLQNFSSDGSAYQWNGQDFTKKENSGNLGFNWINPSKRVRKEQTYSVDNYYK DVLKQPLTIKEKPQKQTVFKPKAPKAYTFQDHQFAPAGLEPLLEREQLNFKKDTNFQYTV DDFGDSDEEFLVDEDKDELSREDKCKIEQEKIDNVEPLTEEETILKDKLLNESFHTWSRR DFTNFIHATAKYGRDAYAKIAKALGNKTTNEVKRYATKFWASYQQIDGYEKYISQIEAQE KKRDKLMNQQRLLAAKIENLTDPWEDLSIVYPPNNSKRIYSKTEDKFLLNCVYKYGINDE RLNEKIRHEIQNSDVFKFDWFIQSRTSQEIGRRVNTLLLAITREMEGPPANKKRKLLGSA SSNSSSRVGSVEPGVGSEKAWSEVPAK BLAST Read more here: Source link

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ASM361163v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::09/28/2018 18:16:55 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::4.6 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::8,506 CDS (total)::8,444 Genes (coding)::8,247 CDS (coding)::8,247 Genes (RNA)::62 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1 (5S, 16S,…

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ASM491215v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::04/19/2019 21:15:33 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.8 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::5,008 CDSs (total)::4,951 Genes (coding)::4,808 CDSs (with protein)::4,808 Genes (RNA)::57 rRNAs::3, 1, 1 (5S, 16S, 23S) complete rRNAs::3 (5S) partial…

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Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification

Human study The study was approved by the institutional review boards (Ethics Commission of the Medical Faculty of Technical University Munich (protocol 193/17S) and Ethics Committee of the Medical Faculty of Heidelberg University (protocol S-206/2011)) and all patients provided written informed consent under these protocols. The study was conducted in…

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How to extract protein sequences from a .gff file

Hello everyone! I am a beginner with bioinformatics but at the company I work at we have a genome assembly of one of our crops. I wanted to annotate the genome and to do so I used a piece of python code in ubuntu. I used the Augustus Arabidopsis database…

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RefSeq: NC_009613 CDS #1407

RefSeq: NC_009613 CDS #1407 >NC_009613 (refseq) 1635855..1636985 /translation= MITIKEAKTKKELTDYIKFPFSLYKNNKYWVPPIIDDELETFDKTKNPAFENAEAYFYLA YRDNKIVGRIAAIINWSEVNDQQKSKVRFGWFDVIDDIEVTKILLEKVRELGKKNNLDHI EGPMGFSNLDKVGVLTEGFEEIGTMITWYNFPYYAIHFEQLGFVVEKEYLENKFPFANVK LEFFDKAQELIKRRYNLKALNFKKTKDVLPYVDKMFDLFNASYANLSSFVAISDIQKEYF KKKYISFINPEYIKFVEDKDQNLVAFAIVMPSFSRALQKAKGKLFPFGLFHLLNARKNSK DVTFYLIGVHPEYQNKGVHAIIFKEMHTTFTEKGIKNCIRTPELADNHAIHLLWKNFDPK IICRRKTFRIQISDFR BLAST Read more here: Source link

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ASM969558v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::09/10/2019 03:25:17 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.9 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::2,851 CDSs (total)::2,768 Genes (coding)::2,716 CDSs (with protein)::2,716 Genes (RNA)::83 rRNAs::5, 4, 5 (5S, 16S, 23S) complete rRNAs::5 (5S) partial…

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RefSeq: NC_009613 CDS #1732

RefSeq: NC_009613 CDS #1732 >NC_009613 (refseq) 1997084..1998784 /translation= MKPIYLLIPLIVFICCKKNTLDKNPDNSSFIHFPFLNYSVKIDSVVISNLNNPNLVAFYK NYNNETVWVLEEDRTAVLNEFKDATNEGLLPNDYNYTLLNTLSSNYNHLEDNKLIEFDLL LTQSIQKYISHIYKGKINPRTIYKDWDLKEKNIDINTVLFEIIEKKSFASKFEDLKPKHP IYKNLKQALQVLNAFPKDSVPFVILKPKDKIALNKSNKAVKIIKSRLMYWHDMKQANTIT NIYDKETQDAVKTFQSRHGLTPDGLIGKGTILALNFTKNQRIEQVISNLERWRWFASDFG QNYLLINIPDYSLLAIKNNDTMQKQRIVVGKDTRQTPILESKVSNINLNPNWTVPPTILK EDIYPDAIKDKGAFKKKGLVILDHKNKEINPWSWTIEDAKKYKYVQNPGKNSSLGLMKIN FPNKYSVYLHDTNHRDFFGLNYRSLSSGCVRLEKPLEMAEYLINNPEKWNLKTIQDTTDI NHYNKLQKEKEKKIAIKNAKLLAKNPLLVIPEKTYPKQELKTIVVRIADDIFIHQLYWTA WLQKETLQFREDIYCLDSDLYNKLRN BLAST Read more here: Source link

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A genome catalogue of lake bacterial diversity and its drivers at continental scale

Newton, R. J., Jones, S. E., Eiler, A., McMahon, K. D. & Bertilsson, S. A guide to the natural history of freshwater lake bacteria. Microbiol. Mol. Biol. Rev. 75, 14–49 (2011). Article  CAS  PubMed  PubMed Central  Google Scholar  Pernthaler, J. Competition and niche separation of pelagic bacteria in freshwater habitats….

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RefSeq: NC_017831 CDS #1941

RefSeq: NC_017831 CDS #1941 >NC_017831 (refseq) 2153445..2155646 /translation= MPAASPPSAAPPQSAGAAFVASMSDWARTDGAAWLYLAKALAAAFLALGVSMVLDLPAPK TAMTTVFIVMQPQSGAVFAKSFYRLIGTFVGLTATLALVGLFPQQPVLFLLAVALWVAAC TAGAARNRNFRSYGFLLAGYTAALIGLPASQAPNGAFMTAMTRVSEISVGILSAGIVSAL IFPQYTGEQMRTTVRRRFGAFVDYVAAALAGALDRSKIESVHTRFVADVVGFEAARSMAV FENPDTRMRSGRLSRLNSEFMTASSRFHSLHQLMNRLHATSAQAVDALEPYFREIAPLLS NDGDHVRTSADAARAAEQLLAYRDALPRRIRATRAEHETQPAFPLLDFDTASELLYRFIT DLHAYAATYASLAASTHARERWIERYEPRTNATAALIAGIRTASVMLLLSVFWIYSAWPS GVMLVLNAAAVCALASSSPQPTRMAAQMALGTAFAVATGFVLMFGVYPHIDGFVLLCAAL APFLAPGVLMSLKPKYAGCGAGYLIFFCTLAGPENLTHYDPIGFMNDALALVLSMIVSAI AFAVLFPPSAPWLKKRLFADLRHQAVAACHARLPGLRTRFESGARDLMFQAHGLSADQPD AQRDALRWMFAVLETGNAVIDLRHELAALPRDPRYAATMPWRRKIEAARDALAALFDKPA PARFDAALAAAVDAIAATQQALVAFAPPREERHQMQRILSQLHFVRTALLDPESPLAALN GARTPTDRPGVSS BLAST Read more here: Source link

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ASM2097156v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::06/02/2023 00:23:34 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::6.5 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA Genes (total)::4,271 CDSs (total)::4,166 Genes (coding)::4,002 CDSs (with protein)::4,002 Genes (RNA)::105 rRNAs::8, 7, 7 (5S, 16S, 23S) complete rRNAs::8, 7, 7…

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RefSeq: NC_007494 CDS #559

RefSeq: NC_007494 CDS #559 >NC_007494 (refseq) complement(610715..612310) /translation= MSPQYDAIIVGGGHNGLTCGAYLARAGVKVLVVERQPMVGGAAVTGEIAPGYRSSLASYY QGLLQPKVILDLELQKYGFEVIPAAPTVFALEGGRTFTLWDDPEKFAAEIAKFSNVDGAA YAGYRAHMLKIAPHMKQLLWEVPVDPASGKIRDLKRLAGFVWRFRKVGPQFYDIYNLLTM SAWDYLSRWFTSDEVKLVLGFFAGGGGANSSLKTPGSAYMLARGIVRDGGTAAGPAGFMK GGMGAISEAIRRSGEAHGMEVRTACPVERILVENGRAVGVRLEGGEEIRSKIVIANATAR TTFTKLLDPAELPEEFNRDIRNIRCESTVFRVNLALSALPEAPVFGQTNPQGSIVPQMTV APNVAYMERAWHQAQGGEIAEAPFLIVKVPSMVDPTLAPEGHHIMNVFGGHAPYTLARGD WDSRREELWGRVLAVLKTQFPDIESRILHRQIMTPLDLERIFDLPNGHVHHGEISADQMF FRRPSPQFADYRSPVDRLYQASASVHPGGGVTGVPGHNAAKVILEDRRKWS BLAST Read more here: Source link

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ASM2078331v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::10/07/2022 02:25:48 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; repeat_region Genes (total)::2,910 CDSs (total)::2,860 Genes (coding)::2,857 CDSs (with protein)::2,857 Genes (RNA)::50 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1,…

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ASM1130205v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::05/06/2023 01:03:55 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::6.5 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA Genes (total)::2,160 CDSs (total)::2,109 Genes (coding)::2,092 CDSs (with protein)::2,092 Genes (RNA)::51 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1…

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Comment: search for intron conservancy across species

the process of calculating conservation scores does not, so far as i am aware, change dependent upon functional annotations I’m not interested in functional annotation, I didn’t mention it. Not sure why it might be related to my question. 1) generate multiple sequence alignment Once again, my aim is to…

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reference annotation for the human and mouse genomes in 2023

D942–D949 Nucleic Acids Research, 2023, Vol. 51, Database issue Published online 24 November 2022 doi.org/10.1093/nar/gkac1071 GENCODE: reference annotation for the human and mouse genomes in 2023 Adam Frankish 1,* , Sı́lvia Carbonell-Sala2 , Mark Diekhans 3 , Irwin Jungreis 4,5 , Jane E. Loveland 1 , Jonathan M. Mudge1 ,…

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Filtering CDS from a full mitogenome

Filtering CDS from a full mitogenome 0 Hello everyone, I have several sequences of the whole mitochondrial genome of the Yellow Crazy Ant and I also have (from NCBI: www.ncbi.nlm.nih.gov/nuccore/NC_039576.1) the annotation of the genome. I would like to filter my full sequences to leave only the protein-coding sequences from…

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Monocle3 error when passing gene_module_df directly to plot_cells()

Monocle3 error when passing gene_module_df directly to plot_cells() 0 Hello I’m a new computational biologist and I’m following the Monocle3’s guide on finding modules of co-regulated genes cole-trapnell-lab.github.io/monocle3/docs/differential/#gene-modules But when I run the plot_cells() function, it keeps showing an error after I pass gene_module_df directly to plot_cells(): Error in !is.null(dim(genes))…

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Help with htseq -count read counts

Hello I am doing a transcriptome analysis on Pseudomonas putida and I have been trying to do a read count using Htseq -count. The program always give an error. I have tried different genome references (fna) and annotation files (gtf ang gff) but it does not work. The mapping works…

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r – Adding variants from amplicon sequenced data to MAF file generated by WES data

I am relatively new to bioinformatics, and I need some help with adding variants from a specific gene that were sequenced using amplicon data (due to bad sequencing in a hot spot) to a MAF (Mutation Annotation Format) file. The MAF file I have is entirely generated from WES (Whole…

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Characterization of crAss-like phage isolates highlights Crassvirales genetic heterogeneity and worldwide distribution

Isolation of crAss-like phages CrAss-like phages were searched in 12 sewage samples from five wastewater treatment plants using three different qPCR assays, the one designed from ΦCrAss001 genome in this study and two previously described12,19. Depending on the qPCR assay employed and the samples, values in wastewater ranged from 103−106…

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ASM1313180v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::05/19/2020 07:11:15 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.11 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::7,496 CDSs (total)::7,428 Genes (coding)::7,326 CDSs (with protein)::7,326 Genes (RNA)::68 rRNAs::4, 5, 3 (5S, 16S, 23S) complete rRNAs::1, 1 (5S,…

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Cryomorphaceae_CECT30217 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::09/04/2022 11:55:32 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)::3,569 CDSs (total)::3,527 Genes (coding)::3,502 CDSs (with protein)::3,502 Genes (RNA)::42 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1,…

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adding features to gtf file using agat tool function

I m trying to use this agat which adds new attributes from tsv to gtf file. My file formats are as such input tsv which is my reference file gene_id Entrez_ID ENSCAFG00845006432 399518 ENSCAFG00845002136 399530 ENSCAFG00845029798 399544 ENSCAFG00845011460 399545 ENSCAFG00845001610 399653 ENSCAFG00845013158 403157 ENSCAFG00845014982 403168 ENSCAFG00845021967 403170 ENSCAFG00845019241 40340 Next…

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ASM2328384v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::01/20/2022 16:35:44 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)::4,276 CDSs (total)::4,140 Genes (coding)::4,114 CDSs (with protein)::4,114 Genes (RNA)::136 rRNAs::8, 6, 5 (5S, 16S, 23S) complete rRNAs::3, 1 (5S,…

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ASM2091172v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::12/10/2022 05:46:01 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)::3,525 CDSs (total)::3,413 Genes (coding)::3,361 CDSs (with protein)::3,361 Genes (RNA)::112 rRNAs::9, 9, 9 (5S, 16S, 23S) complete rRNAs::9, 9, 9…

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ASM528147v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::10/06/2022 04:12:32 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; repeat_region Genes (total)::4,755 CDSs (total)::4,698 Genes (coding)::4,670 CDSs (with protein)::4,670 Genes (RNA)::57 rRNAs::4, 4, 4 (5S, 16S, 23S) complete rRNAs::4, 4,…

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mRNA Vaccines for Rapid Response to Biological Threats

COVID-19 demonstrated the enormous dangers posed by biological threats, severely impacting virtually every community in the world. Mitigating these risks in the future is an urgent global imperative. To that end, the National Biodefense Strategy and Implementation Plan, published by the U.S. government in October 2022, outlines goals for countering…

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ASM1988058v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::08/31/2021 18:47:03 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.2 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::5,924 CDSs (total)::5,867 Genes (coding)::5,840 CDSs (with protein)::5,840 Genes (RNA)::57 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1…

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Coding sequence

Coding sequence 1 How to do the below analysis in practice? Some CDS were obtained from databases that provide the genome, while others are extracted based on custom Perl scripts. sequence Coding • 77 views You could look into UCSC table browser to extract CDS sequences from reference genomes (databases…

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ASM362665v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::10/01/2018 17:55:31 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::4.6 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::6,630 CDS (total)::6,537 Genes (coding)::6,350 CDS (coding)::6,350 Genes (RNA)::93 rRNAs::3, 3, 1 (5S, 16S, 23S) complete rRNAs::3, 1, 1 (5S, 16S,…

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Bioinformatics Engineer (SEII) Job – Karkidi

Key Skills AWS, Bash scripting, Bioinformatics, Containerization, Debugging, Docker, Effective communication skills, Java Programming, Linux Operating system, Python Programming, R Programming, UI design, UX design Job Description Bioinformatics Engineer (SEII) About Catalytic Data Science (CDS):  REMOTE OPPORTUNITY  Catalytic Data Science is a groundbreaking cloud R&D platform designed to integrate the…

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ASM2840176v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::01/27/2023 18:34:34 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)::8,960 CDSs (total)::8,883 Genes (coding)::8,725 CDSs (with protein)::8,725 Genes (RNA)::77 rRNAs::3, 1, 3 (5S, 16S, 23S) complete rRNAs::3, 1 (5S, 16S)…

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Rapid detection of fluoroquinolone resistance in Mycobacterium tuberculosis using a novel multienzyme isothermal rapid assay

Global tuberculosis report 2022. Geneva: World Health Organization; 2022. licence: cc bY-Nc-sa 3.0 iGo. WHO operational handbook on tuberculosis. Module 4: treatment – drug-resistant tuberculosis treatment. Geneva: World Health Organization; 2020. Licence: CC BY-NC-SA 3.0 IGO. Chien JY, Chiu WY, Chien ST, Chiang CJ, Yu CJ, Hsueh PR. Mutations in…

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rna seq – building custom gtf file with entrez ID for any organism

How do I generate a custom gtf file format for a organism of my interest similar to human gtf file, in the custom gtf file I want to add entrez id to the new custom gtf. My organism is canis_familaris I have to use is this source. How do I…

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ASM347020v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::08/29/2018 09:42:55 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::4.6 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::3,588 CDS (total)::3,537 Genes (coding)::3,480 CDS (coding)::3,480 Genes (RNA)::51 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1 (5S, 16S,…

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ASM2855059v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::02/02/2023 13:08:25 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)::3,408 CDSs (total)::3,351 Genes (coding)::3,302 CDSs (with protein)::3,302 Genes (RNA)::57 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1 (5S,…

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How to add “transcript” feature to a gtf file?

How to add “transcript” feature to a gtf file? 0 I have a gtf file that looks as follows (lines for transcript ENSMUST00000027477): protein_coding exon 87510093 87510362 . – . gene_id “ENSMUSG00000026259”; transcript_id “ENSMUST00000027477”; exon_number “1”; gene_name “Ngef”; gene_biotype “protein_coding”; transcript_name “Ngef-002”; exon_id “ENSMUSE00000342435”; 1 protein_coding CDS 87510093 87510199 ….

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ASM799306v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::08/07/2019 18:48:10 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.8 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::3,757 CDSs (total)::3,703 Genes (coding)::3,643 CDSs (with protein)::3,643 Genes (RNA)::54 rRNAs::1, 1, 3 (5S, 16S, 23S) complete rRNAs::1, 1, 1…

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ASM1258445v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::04/15/2020 13:52:50 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.11 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::4,459 CDSs (total)::4,385 Genes (coding)::4,312 CDSs (with protein)::4,312 Genes (RNA)::74 rRNAs::1, 2, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1…

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shRNA Adeno-associated Virus Serotype 2, p7SK-(JOSD2-shRNA-Seq1) (AAV-SI1373WQ)

Online Inquiry For Research Use Only. Do NOT use in humans or animals. For Research Use Only. Do NOT use in humans or animals. This product is a JOSD2-shRNA encoding AAV, which is based on AAV-2 serotype. The JOSD2 gene encodes a protein containing a Josephin domain. Josephin domain-containing proteins…

Continue Reading shRNA Adeno-associated Virus Serotype 2, p7SK-(JOSD2-shRNA-Seq1) (AAV-SI1373WQ)

ASM2307835v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::02/06/2023 20:43:49 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)::4,891 CDSs (total)::4,832 Genes (coding)::4,569 CDSs (with protein)::4,569 Genes (RNA)::59 rRNAs::3, 3, 3 (5S, 16S, 23S) complete rRNAs::3, 3, 3…

Continue Reading ASM2307835v1 – Genome – Assembly

RefSeq: NC_014408 CDS #37

RefSeq: NC_014408 CDS #37 >NC_014408 (refseq) complement(35145..36620) /translation= MKYRCKVCDYIYDPEVGDPTSGIKPGTPFQELPEDWLCPVCNVGKDQFEPLRGEVRRVRP EDIDMFCYQCSQTVRGRACTVKGVCGKEATVARLQDNLLFAIKGISAYLYHARELGYTDE VVDAFLERGFYSTLTNVNFDAEEFVSLALEAGEMNLRTMKLLKKAHMDTYGEPEPAEVRV GALDGPAIIATGHSLKALEELLKQTEGSGVNVYTHSELLPAHGYPGLRKYPHLAGQLGGP WFDQRETFSRYSAAVLGTSNCVLLPRDSYRDRMFTCGVARLPGVEHVDGYDFSPVIEKAL ELPPLKEEDSATLTTGFGLSTILSLADKIKELVEEGKIRRFFLVGGCDSPLPQAKYYTEF VRKLPEDTVVLTLACGKYRFNSMDLGDIDGIPRLIDLGQCNDSIVAVELVEALSNLFSMD VNELPLSIVLSWMEQKAAAILWSLLSLNLRGMYIGPILPGWANDDIINVLVDKYELTPIG DPEEDIKKMME BLAST Read more here: Source link

Continue Reading RefSeq: NC_014408 CDS #37

Regulation of differentially expressed coding and non-coding isoforms

Regulation of differentially expressed coding and non-coding isoforms 0 Hi All, I have a question regarding transcripts that encode proteins and those that encode other products as defined by Ensembl Biotype category (i.e. retained intron CDS not defined Nonsense mediated decay etc). I have included an example of what I…

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ASM1423031v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::08/12/2020 19:48:31 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)::3,706 CDSs (total)::3,649 Genes (coding)::3,630 CDSs (with protein)::3,630 Genes (RNA)::57 rRNAs::2, 2, 2 (5S, 16S, 23S) complete rRNAs::2, 2, 2…

Continue Reading ASM1423031v1 – Genome – Assembly

phylogenetics – Pal2nal translation of large multi-fasta files produces a codon translated file where some sequences half length of the average

I did sequence alignment of a large peptide multi-fasta (n= 4991 sequences). The peptide alignment has sequences with the same length and pal2nal went through just fine… except some of the codon sequences are at half length. If average is X then some sequences are X/2. This is choking IQ-Tree….

Continue Reading phylogenetics – Pal2nal translation of large multi-fasta files produces a codon translated file where some sequences half length of the average

Pal2nal translation of large multi-fasta files produces a codon translated file where some sequences half length of the average.

Pal2nal translation of large multi-fasta files produces a codon translated file where some sequences half length of the average. 0 I did sequence alignment of a large peptide multi-fasta (n= 4991 sequences). The peptide alignment has sequences with the same length and pal2nal went through just fine… except some of…

Continue Reading Pal2nal translation of large multi-fasta files produces a codon translated file where some sequences half length of the average.

ASM202738v1 – Genome – Assembly

##Genome-Annotation-Data-START##Annotation Provider::NCBIAnnotation Date::07/14/2014 10:14:21Annotation Pipeline::NCBI Prokaryotic Genome Annotation PipelineAnnotation Method::Best-placed reference protein set; GeneMarkS+Annotation Software revision::2.6 (rev. 439576)Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_regionGenes::5,815CDS::5,702Pseudo Genes::37CRISPR Arrays::2rRNAs::6 (5S, 16S, 23S)tRNAs::69ncRNA::1Frameshifted Genes::32##Genome-Annotation-Data-END## Read more here: Source link

Continue Reading ASM202738v1 – Genome – Assembly

ASM2462242v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::08/05/2022 10:23:45 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)::1,475 CDSs (total)::1,421 Genes (coding)::1,410 CDSs (with protein)::1,410 Genes (RNA)::54 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1…

Continue Reading ASM2462242v1 – Genome – Assembly

RefSeq: NC_007799 CDS #165

RefSeq: NC_007799 CDS #165 >NC_007799 (refseq) complement(193803..195224) /translation= MPKSKHKVRKYSTHSRLRNEIFEILSTDPLKLLLVIVPEVCDVPTADNENYRYHSIIQFY TNTSHKTIQDKKKARLLLKLWFKELINKISDRVIIFPEDQKIIDKALNKLFSNFKNISIT QQTKDTLFKTFRKIILKSDINPELKEFFRSYALDMSSLTMYTREIIKEITSEITSAMNNP DATLLIACHGITGPYSNNYPNIPISQQIRYLYQHIMKIPPINPKTALNLFPKQHIVFSIQ NKLINTRIKLKDHQNKTEKLLRHPYPWYSIINKLKQIIHIYIVKPRITKKTEIIKQIENA FTESIAYGDTTLFFKQLQIIRHNTNISWNPYYKDIKITIRSLSNMEPSAQDTMTIKEFVS NMKFYIKHEHVIYPTRNTTKQHLPSTSYTIREPITTGHNKSRKSNIIKNTKKAILHIAKN STKSIKNKLRKVIRHKKTKSYEKLITPSTNFTFLDSTSSIKSTHTQPSTSTSL BLAST Read more here: Source link

Continue Reading RefSeq: NC_007799 CDS #165

RefSeq: NC_019386 CDS #1845

RefSeq: NC_019386 CDS #1845 >NC_019386 (refseq) complement(1784367..1785548) /translation= MEALSLLVVLLAYLGLALGGLPGYRMNRAGVALVGASFLVLLGALDLEEAWRALDAHTLV FLFGVMVLNAQLGYAGFFALAVRGLLRLARTPFALLLLLTLGAGGLSALFLNDTMALLLT PLLLGLARGLGLNPVPYLLALMGAVNTGSLMAPTGNPQNIVVASLSGLSYLDFVRALSPV ALFGLLLQVALLALLYPEVRSLRPLPPLPPVRARVHPGLLRKGLLVTLGLLLAFLLGYPM AQGALVAAGLLLFTRRLRSERFFLRVDWELLVMFGGLFVLTEGVRRLGLAEGLLPLAETP LGLLLSSTLLSLLISNVPAVLLLAGHVEGKEAWLLLAGGSTLAGNLTLLASVANLIVAEG AGREGVRLDVWTHLRFGLPLTLLGLGFLYLWLA BLAST Read more here: Source link

Continue Reading RefSeq: NC_019386 CDS #1845

Electrochemical biosensor strategy combining DNA entropy-driven technology to activate CRISPR-Cas13a activity and triple-stranded nucleic acids to detect SARS-CoV-2 RdRp gene

Zhu JJ (2021) Special topic: biomedical application of DNA-assembled nanostructure. J Anal Test 5(2):93–94 Article  Google Scholar  Pan J, He Y, Liu Z, Chen J (2022) Tetrahedron-based constitutional dynamic network for COVID-19 or other coronaviruses diagnostics and its logic gate applications. Anal Chem 94(2):714–722 Article  CAS  PubMed  Google Scholar  Zhang…

Continue Reading Electrochemical biosensor strategy combining DNA entropy-driven technology to activate CRISPR-Cas13a activity and triple-stranded nucleic acids to detect SARS-CoV-2 RdRp gene

RefSeq: NC_001146 CDS #201

RefSeq: NC_001146 CDS #201 >NC_001146 (refseq) 387227..389767 /translation= MELEPTLFGIIEALAPQLLSQSHLQTFVSDVVNLLRSSTKSATQLGPLIDFYKLQSLDSP ETTIMWHKIEKFLDALFGIQNTDDMVKYLSVFQSLLPSNYRAKIVQKSSGLNMENLANHE HLLSPVRAPSIYTEASFENMDRFSERRSMVSSPNRYVPSSTYSSVTLRQLSNPYYVNTIP EEDILKYVSYTLLATTSALFPFDHEQIQIPSKIPNFESGLLHLIFEAGLLYQSLGYKVEK FRMLNISPMKKALIIEISEELQNYTAFVNNLVSSGTVVSLKSLYREIYENIIRLRIYCRF TEHLEELSGDTFLIELNIFKSHGDLTIRKIATNLFNSMISLYYEYLMNWLTKGLLRATYG EFFIAENTDTNGTDDDFIYHIPIEFNQERVPAFIPKELAYKIFMIGKSYIFLEKYCKEVQ WTNEFSKKYHVLYQSNSYRGISTNFFEIINDQYSEIVNHTNQILNQKFHYRDVVFALKNI LLMGKSDFMDALIEKANDILATPSDSLPNYKLTRVLQEAVQLSSLRHLMNSPRNSSVING LDARVLDLGHGSVGWDVFTLDYILYPPLSLVLNVNRPFGRKEYLRIFNFLWRFKKNNYFY QKEMLKSNDIIRSFKKIRGYNPLIRDIINKLSRISILRTQFQQFNSKMESYYLNCIIEEN FKEMTRKLQRTENKSQNQFDLIRLNNGTIELNGILTPKAEVLTKSSSSKPQKHAIEKTLN IDELESVHNTFLTNILSHKLFATNTSEISVGDYSGQPYPTSLVLLLNSVYEFVKVYCNLN DIGYEIFIKMNLNDHEASNGLLGKFNTNLKEIVSQYKNFKDRLYIFRADLKNDGDEELFL LSKSLR BLAST Read more here: Source link

Continue Reading RefSeq: NC_001146 CDS #201

The effect of inhibition of receptor tyrosine kinase AXL on DNA damage response in ovarian cancer

Cell lines and culture conditions All media and supplements were purchased from Gibco unless otherwise stated. OC cell line SKOV3, OVCA429, CH1 and NSCLC cell line H1299 and A549 were maintained using Dulbecco’s Modified Eagle Medium (DMEM) media supplemented with 10% (v/v) foetal bovine serum (FBS). OC cell lines HeyA8,…

Continue Reading The effect of inhibition of receptor tyrosine kinase AXL on DNA damage response in ovarian cancer

How to retrieve gene and CDS entries properly from GenBank files with Perl?

In my goal to write a Perl script without modules that retrieves all simple gene and CDS entries (without the GenBank operators, since I have no clue how to handle them) in a specified range, I’ve come up with the following: use strict; use warnings; my $gene=””; my $CDS =…

Continue Reading How to retrieve gene and CDS entries properly from GenBank files with Perl?

ASM649199v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::06/21/2019 16:31:47 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.8 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::674 CDSs (total)::632 Genes (coding)::623 CDSs (with protein)::623 Genes (RNA)::42 rRNAs::2, 1, 3 (5S, 16S, 23S) complete rRNAs::2 (5S) partial…

Continue Reading ASM649199v1 – Genome – Assembly

ASM480391v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::10/06/2022 04:05:55 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; repeat_region Genes (total)::3,339 CDSs (total)::3,271 Genes (coding)::3,086 CDSs (with protein)::3,086 Genes (RNA)::68 rRNAs::4, 4, 4 (5S, 16S, 23S) complete rRNAs::4, 4,…

Continue Reading ASM480391v1 – Genome – Assembly

Mapping transcript location issue.

Mapping transcript location issue. 0 Hi I have performed target prediction for human sample using miranda tool. From the result obtained i want to check which exact part of transcript is the miRNA binding to (CDS,Exome,UTR..). On checking the mapping coordinates they do not lie in between any exact coordinates…

Continue Reading Mapping transcript location issue.

Use DESeq (1) data with DESeq2 Package?

Use DESeq (1) data with DESeq2 Package? 0 Hey everyone, is there a way to deal with data from DESeq packages in current versions of R (e.g. R 4.3.0). I currently deal with this be using a conda environment with old R and DESeq. Then I just run R from…

Continue Reading Use DESeq (1) data with DESeq2 Package?

Single-cell quantification of ribosome occupancy in early mouse development

PDMS chip fabrication Moulds were 3D-printed by Proto Labs with WaterShed XC 11122 at high resolution (Supplementary Fig. 1). Reusable moulds were assembled by taping 3D-printed molds to glass slides (5″ × 4″; Ted Pella). Sylgard 184 PDMS monomer and curing agent (4019862, Ellsworth Adhesives) were mixed at a 10:1…

Continue Reading Single-cell quantification of ribosome occupancy in early mouse development

RefSeq: NC_009483 CDS #902

RefSeq: NC_009483 CDS #902 >NC_009483 (refseq) complement(1057148..1059157) /translation= MTTTAGKLVDPAFLIITGLILTGFSGVPGLFLKNAAAFGQKLATAFACVGALCGLAGAFS TIASGETEIFVVNWSLPFGPCEIGIDPLAALFLLSVFLISGCSAVYANGYWPAAKLPATS RALCFFIGILSASMALLIIARNSVFFLMAWEVMALSAYFAFTVESGNAEVRKAGMLYLVC THAGTMALFVMFILLRTMTGSFQFASTASLNPLAPGAAVIFFAALFGFGMKAGIMPLHIW LPAAHANGPSHVSAMMSGVMLKMGIYGIIRIISLFYPVPTWWGAVILGLGIISGVTGIIS AIGQNDIKRILAYSSIENIGIITMGIGAAVIGQSIGNQTLVLLGMGGALLHVLNHSLFKS LLFLGSGALIHSVGTRELNRMGGLARRMPRTAPLFLIGAMAICGLPPLNGFISEYLLYFG FFSGVKDGAAPILLGMGLAVTALALIGALALACFVKVYGVAFLGAPRSAEAEQGHDAPWQ MPAAMGLLALCCLVIGLLPQYAAHLVQPAVYAVFPSLVAAGSGITTQAPLGWIGFIGTAL IIAAALLAAGYYRRLKSIPPASATTWGCGYLQPTVRMQYTSTSFAEILVRLFRGTLQPRY ALPKITGFLPASAGFSSRIPETVLDVVILPFLRVTGIVFSFFRRLQNGEQSLYVLYIFIT LVLLMVWAH BLAST Read more here: Source link

Continue Reading RefSeq: NC_009483 CDS #902

Root1293 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::10/29/2015 10:18:10 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::3,379 CDS::3,235 Pseudo Genes::94 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1 (5S, 16S, 23S) partial rRNAs:: tRNAs::46 ncRNA::1 ##Genome-Annotation-Data-END##…

Continue Reading Root1293 – Genome – Assembly

RefSeq: NC_021016 CDS #557

RefSeq: NC_021016 CDS #557 >NC_021016 (refseq) complement(559898..560782) /translation= MKQKKTLQILLLVFAGLIVLYTGVNLYQKQQSSKEDSDQTMISDLKSLTSISYNNNGTTL SFIKQSGKWYYTKNKKYPITQSSLESLASTFQKVEAVRELKNADVLSDYGLDKPTYTVSV KDKTGKSMTYYIGNATGENYYVTYGDKSKIYTVSSDITSSLSYSLDNLIETDTFPTLSTG NLKKVLVTQNGKTKTYTSKKKNLDGISGGLGVFTFGDCQNYYASQTDLVKYGLNKDSRIT VDITYKDTDTKKTKNVVLYIGKKDSDQKNYYVKLKGSHMVYLSDKDVVKNILNP BLAST Read more here: Source link

Continue Reading RefSeq: NC_021016 CDS #557

ASM2794617v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::05/11/2023 07:01:11 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::6.5 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA Genes (total)::2,040 CDSs (total)::1,986 Genes (coding)::1,973 CDSs (with protein)::1,973 Genes (RNA)::54 rRNAs::3, 3, 3 (5S, 16S, 23S) complete rRNAs::3, 3, 3…

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Selecting CDS from genbank file interval

Selecting CDS from genbank file interval 0 Hello, I tried writing a script in perl that extracts from two parameters the CDS portions with their description and output them in a .txt file, but it just comes out empty. Help! #!/usr/bin/perl use strict; use warnings; # Get the interval data…

Continue Reading Selecting CDS from genbank file interval

ASM1806992v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::04/13/2021 09:55:22 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.1 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::3,045 CDSs (total)::2,994 Genes (coding)::2,979 CDSs (with protein)::2,979 Genes (RNA)::51 rRNAs::1, 1, 2 (5S, 16S, 23S) complete rRNAs::1, 1 (5S,…

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Uploading 10x Data into R for Monocle 3

Uploading 10x Data into R for Monocle 3 1 Hi, I am having trouble loading the cell ranger data into R. I am a beginner, so please excuse my lack of knowledge of R and other terminology. Here is what shows up on my script. cds <- load_cellranger_data(“C:/Users/myname/Downloads/10x_data”) Error in…

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RefSeq: NC_010334 CDS #275

RefSeq: NC_010334 CDS #275 >NC_010334 (refseq) 323130..324341 /translation= MPLSLAAAELQHHGHLKYEYDGYAFSDSSVYQARYGQHQVNQTAQLRYHLGSRWQSGWLV EVDYQLLAGYGEHRFQATPLMNGYLGLSSVIDDELRLFNLTNTLSEHRDFVMLQRLDRAI VGYQTDNNVVKFGRQAITWGNGQFFNPMDFVNPFDPASLDKEYKTGDDMVYGQHLLQDGS DLQAAYVIRRDGDSDITADVATLALKYHGFIDYIYEYDLLLAEHYDNTVAGVSSIISVGG AIWATDLVATWGETNYLSLVSNWGYSWVGFERNMSGTLEYFYNGLGISDGDYSPESLLQH PELVAKIERGELYNLARHYLTGSLYIEMTPLWSVSQNLFYNASDNSALYQVLSQNSLSDE LRLTTALTVPIGANGTEYGGLKFSDGQYFSFELLLYAQLAWYF BLAST Read more here: Source link

Continue Reading RefSeq: NC_010334 CDS #275

RefSeq: NC_014925 CDS #1176

RefSeq: NC_014925 CDS #1176 >NC_014925 (refseq) complement(1239143..1240432) /translation= MKKIMINGPLIGEASVPGDKSMTHRAIMLASLAQGHSVIHQPLLGEDCLRTAKIFEKLGV KMDITDEAITIDSPGYAHFQTPHQTLYTGNSGTTTRLMAGLLGGLGIQSVLSGDASIGKR PMDRVLQPLRQMNVNISGVEDNYTPLIIGSSKVKGIHYEMPVASAQVKSAILFASLFAQN TTTIREIDLSRNHTETMFAHYGIPVQTQDLTVTLPGEGIHHIQPRDFDVPGDISSAVFLI VAALITPGSDITLHNVGINPTRDGIIEIVERMGGKISLSNQTNGPEPTATIRVQYTDDLK GIEIGGSLIPRCIDELPTIALLCTQAHGSSIIKDAEELKVKETNRIDTTANELGKLGLKL EPTDDGLIIKPSTISQIQPVDSHNDHRIGMMLAVASLMTPEPIEIAQFESVNVSFPGFLP LLKQLENEG BLAST Read more here: Source link

Continue Reading RefSeq: NC_014925 CDS #1176

Scoping review of Culex mosquito life history trait heterogeneity in response to temperature | Parasites & Vectors

Zell R. Global climate change and the emergence/re-emergence of infectious diseases. Int J Med Microbiol IJMM. 2004;293:16–26. PubMed  Google Scholar  Gage KL, Burkot TR, Eisen RJ, Hayes EB. Climate and vectorborne diseases. Am J Prev Med. 2008;35:436–50. Article  PubMed  Google Scholar  Elbers ARW, Koenraadt CJM, Meiswinkel R. Mosquitoes and Culicoides…

Continue Reading Scoping review of Culex mosquito life history trait heterogeneity in response to temperature | Parasites & Vectors

IMG-taxon 2698536943 annotated assembly – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::10/05/2022 16:45:12 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; repeat_region Genes (total)::3,571 CDSs (total)::3,513 Genes (coding)::3,464 CDSs (with protein)::3,464 Genes (RNA)::58 rRNAs::3, 3, 3 (5S, 16S, 23S) complete rRNAs::3, 3,…

Continue Reading IMG-taxon 2698536943 annotated assembly – Genome – Assembly

Gene prediction in the era of long read sequencing data and many reference genomes

With the availability and affordability of long read sequencing it has become possible to create many reference genomes. For individuals of the same species, or for many species. See e.g. how Hifiasm can be used with a single command to create a reference genome in a few hours or days…

Continue Reading Gene prediction in the era of long read sequencing data and many reference genomes

Characteristics of molecular markers associated with chloroquine resistance in Plasmodium vivax strains from vivax malaria cases in Yunnan Province, China | Malaria Journal

Sample amplification information and PCR product amplification sequencing A total of 753 cases infected with mono-P. vivax were diagnosed and confirmed in Yunnan Province in 2014, 2020, 2021, and 2022. The patients were predominantly young adult males (84.0%, 632/753), with a smaller number of females (16.0%, 121/753); 81.8% (616/753) of…

Continue Reading Characteristics of molecular markers associated with chloroquine resistance in Plasmodium vivax strains from vivax malaria cases in Yunnan Province, China | Malaria Journal

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

Continue Reading RefSeq: NC_010572 CDS #2537

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…

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

Vancomycin intermediate-resistant Staphylococcus haemolyticu | IDR

Wanyang Dong,1,&ast; Qi Peng,1,&ast; Xiaohua Tang,1,2,&ast; 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…

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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…

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

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…

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

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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