Tag: BLAST

(MENAFN– GlobeNewsWire – Nasdaq) The Global Bioinformatics Market was valued USD 10.23 Billion in 2023 and projected to reach USD 28.6 Billion by 2030, growing at a CAGR of 13.73% during the forecast period of 2023-2030 Richmond, Feb. 09, 2024 (GLOBE NEWSWIRE) — According to a research report ” Bioinformatics…

Richmond, Feb. 09, 2024 (GLOBE NEWSWIRE) — According to a research report “Bioinformatics Market”, by tools Type (BLAST, BioPerl, InterMine, Others), Services (Genome Sequencing, RNA sequencing, Metagenomic Analysis, Epigenomic, Others), Application (Drug discovery, Personalized medicine, Preventive medicine, Transcriptions, Metabolomics, Gene therapy, Others) Sectors (Medical Biotechnology, Animal Biotechnology, Plant Biotechnology, Environmental…

Provided by: roary_3.13.0+dfsg-1_all NAME Bio::Roary::External::Makeblastdb – Wrapper around NCBIs makeblastdb command VERSION version 3.13.0 SYNOPSIS Take in a fasta file and create a temporary blast database. use Bio::Roary::External::Makeblastdb; my $blast_database= Bio::Roary::External::Makeblastdb->new( fasta_file => ‘contigs.fa’, exec => ‘makeblastdb’ ); $blast_database->run(); METHODS output_database Returns the path to the temporary blast database files…

In an extremely proud moment for Odisha, a team of researchers at the prestigious Institute of Life Sciences (ILS) in Bhubaneswar has made a groundbreaking discovery that suggests the role of direct interaction of circRNAs with mRNAs in gene expression regulation. The findings represent a novel method for illuminating the…

About the tool The FASTA format is a text-based format for representing nucleotide or peptide sequences. The FASTQ format additionally includes the corresponding quality scores. This tool allows you to convert FASTQ files to FASTA. The resulting FASTA file will contain only the sequence data from the input FASTQ file….

Identification of putative anti-crispr proteins using structural features To identify Acrs in phage genomes, we began by retrieving ~66.5 million proteins from Integrated Microbial Genomes Virus database (IMG/VR)37. We excluded large proteins because over 90% of known Acrs contain less than 200 amino acids38 (Fig. 1A, Supplementary Data 1). To reduce computational…

Animals and samples The study included 10 pigs, 8 pigs were bred at the INRAE experimental farm (doi.org/doi.org/10.15454/1.5572415481185847E12) and 2 pigs come from breeding organizations in accordance with the French and European legislation on animal welfare. The animals belong to the same family, except for one LW animal. Animals were…

A few hours before the CASP14 (14th Critical Assessment of Structure Prediction) meeting, the latest biannual structure prediction experiment where participants build models of proteins given their amino acid sequences, this image went viral on twitter. Ranking of participants in CASP14, as per the sum of the Z-scores of their…

From nucleotide or proteine sequences to EC number using biopython 0 Hi, if I have a fasta file containing nucleotide sequences or proteines sequences is it possible to get EC number using biopython for example 1.1.1.169 1.1.1.205 1.1.1.25 1.1.1.302 1.1.1.330 1.1.1.34 ps : I’m working on fungus so I need…

Introduction: DNA sequence alignment is a fundamental technique in bioinformatics used to compare and analyze genetic sequences. In this article, we’ll explore a C++ implementation of a basic DNA sequence alignment algorithm, shedding light on its significance and applications in biological research. Background: DNA sequencing is a technique used to…

Pharmaceutical cell biology Uppsala University Bioinformatics computer lab Student name: 1. Sequence alignment using BLAST You are provided with a file named ‘sequences.txt‘, containing a sequence named ‘Sequence1’, extracted from a viral sample. Your task is to identify the type of virus from which this sequence originates. Visit the NCBI…

Tool:Dot_plot_like_in_BLAST, a standalone tool for making dot plots similar to what online BLAST makes 0 The online BLAST (blast.ncbi.nlm.nih.gov) makes dot plots which look like this: Unfortunately, the standalone BLAST lacks the capability of making dot plots. I have made a tool, named Dot_plot_like_in_BLAST, specifically for this purpose. Basically, it…

Nagpur: DNA analysis of severed body parts is underway at a war-footing at the Regional Forensic Science Laboratory (RFSL) to identify the nine victims who were killed in a high explosive TNT blast at the Solar Industries India Limited at Kondhali, around 50 km from Nagpur, on Sunday.The analysts are…

Analysis of the multisegmented nature of BcssDV1 genome B. cinerea field isolates were previously obtained from infected grapes of vineyards of Italy and Spain and their mycovirome was determined [8]. A new ssDNA virus (BcssDV1, Genbank accession no. MN625247) was discovered and characterized. The sequence previously characterized of BcssDV1 (from…

Faculty and trainees from the University of Chicago Medicine Comprehensive Cancer Center (UCCCC) joined the world’s largest hematology community to discuss the latest updates in blood cancers at the 65th American Society of Hematology (ASH) Annual Meeting and Exposition held December 9-12, 2023 in San Diego and online. At the meeting,…

Background Myelofibrosis (MF) is characterized by bone marrow fibrosis, anemia, splenomegaly and MF-associated symptoms. These hallmarks result from dysregulation of the JAK/STAT pathway and BET-mediated MF target gene modulation. Pelabresib (CPI-0610; pela) is an investigational oral small-molecule drug designed to inhibit BET-mediated gene transcription involved in MF pathogenesis. Preclinical data…

Alston JM, Sambucci O. Grapes in the world economy. In: Cantu D, Walker MA, editors. The grape genome. Springer International Publishing; 2019. p. 1–24. Google Scholar  Rahemi A, Dodson Peterson JC, Lund KT. Grape rootstocks and related species. Cham: Springer International Publishing; 2022. Walker MA, Heinitz C, Riaz S, Uretsky…

Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data, especially genetic data. With the advances in biotechnology and sequencing technologies, a huge amount of biological and genetic data is being generated each day which needs to be analyzed using computational techniques. This is where…

Associated RNAi Experiments Homology BLAST of hypothetical protein LOTGIDRAFT_99224 partial vs. L. salmonis genes Match: EMLSAG00000006769 (supercontig:LSalAtl2s:LSalAtl2s379:476161:478870:-1 gene:EMLSAG00000006769 transcript:EMLSAT00000006769 description:”maker-LSalAtl2s379-augustus-gene-4.10″) HSP 1 Score: 59.6918 bits (143), Expect = 4.225e-12Identity = 29/57 (50.88%), Postives = 39/57 (68.42%), Query Frame = 0 Query: 22 AANARERTRMRVLSKAFGRLKLTLPWVPPDTKLSKLDTLRLATSYISHLQRLLSDEE 78 +N +ER R + ++…

Crous, P. W. et al. Fungal Planet description sheets: 214–280. Persoonia 32, 184–306 (2014). Article  PubMed  PubMed Central  Google Scholar  Zhang, Y. et al. Multi-locus phylogeny of Pleosporales: A taxonomic, ecological and evolutionary re-evaluation. Stud. Mycol. 64, 85–105 (2009). Article  PubMed  PubMed Central  Google Scholar  Schoch, C. L. et al….

. 2023 Dec 15;133(24):e173959. doi: 10.1172/JCI173959. Item in Clipboard Amanda Macamo et al. J Clin Invest. 2023. Show details Display options Display options Format AbstractPubMedPMID . 2023 Dec 15;133(24):e173959. doi: 10.1172/JCI173959. Item in Clipboard Cite Display options Display options Format AbstractPubMedPMID No abstract available Keywords: Brain cancer; Oncology; Virology. PubMed Disclaimer…

Otto, S. P. & Whitton, J. Polyploid incidence and evolution. Annu. Rev. Genet. 34, 401–437 (2000). Article  CAS  PubMed  Google Scholar  Van de Peer, Y., Maere, S. & Meyer, A. The evolutionary significance of ancient genome duplications. Nat. Rev. Genet. 10, 725–732 (2009). Article  PubMed  Google Scholar  Comai, L. The…

Intel released Core Ultra CPUs Thursday, the first chips to include onboard neural processing units that allow laptops to take on specialized AI tasks. The chipmaker said that some manufacturers offer the Core Ultra now; the new chips will be available in more than 230 different laptop models in…

  Q&A Report from the workshop: QuestonWha is he bes msa ool?clusal 2 and clusal omega are he sameHow would we ener multple sequences? because here is only one inpu boxCould he legend explaining symbiols (*, -,…) be shown in he resul window?Wha is he max number of sequences one…

Whole genome sequencing and analysis To understand the mechanisms underlying the biological control capability of bacterial pathogens, the complete genome of MEP218 was sequenced, assembled, and deposited in the GenBank database under the accession number CP042864.2. The genome of MEP218 consists of a single circular chromosome of 3,944,892 bp with a…

1Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan 2Department of microbiology, Faculty of medicine, university of Khartoum, Sudan 3Head department of biotechnology, Biotechnology Park, Africa city of technology, Sudan 4Botany department, Faculty of Science, University of Khartoum, Sudan American Journal of Microbiological Research. 2014, Vol. 2 No. 6, 217-223DOI:…

Is it possible to obtain all bacterial assemblies from RefSeq and GenBank that contain a specific gene? 0 Hello, I am trying to do some analysis on bacterial assemblies containing a particular AMR gene. I tried searching through NCBI genbank, refseq and it does not give me all the assemblies….

Exercise 1:Finding an unknown gene. Your supervisor has conducted a PCR experiment and given you an unknown sequence for analysis. The sequence is as below: >Unknown_sequence_1 AAATGAGTTAATAGAATCTTTACAAATAAGAATATACACTTCTGCTTAGGATGATAATTG GAGGCAAGTGAATCCTGAGCGTGATTTGATAATGACCTAATAATGATGGGTTTTATTT CCAGACTTCACTTCTAATGGTGATTATGGGAGAACTGGAGCCTTCAGAGGGTAAAAT TAAGCACAGTGGAAGAATTTCATTCTGTTCTCAGTTTTCCTGGATTATGCCTGGCAC CATTAAAGAAAATATCATCTTTGGTGTTTCCTATGATGAATATAGATACAGAAGCGTCA TCAAAGCATGCCAACTAGAAGAGGTAAGAAACTATGTGAAAACTTTTTGATTATGCAT ATGAACCCTTCACACTACCCAAATTATATATTTGGCTCCATATTCAATCGGTTAGTCTA CATATATTTATGTTTCCTCTATGGGTAAGCTACTGTGAATGGATCAATTAATAAAACACA TGACCTATGCTTTAAGAAGCTTGCAAACACATGAA Guidelines to conduct sequence analysis 1. Navigate to the main BLAST page (blast.ncbi.nlm.nih.gov/Blast.cgi) 2. Select…

How to run diamond blastp to get all vs all similarity score between proteins? 0 Hi. I have a .fa file representing multiple predicted proteins. Example: >NC_001341.1_1 # 397 # 714 # 1 # ID=1_1;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.314 MCSSSIISEKHLKKNIFQKKAKVQYKIKKNRRGQINENKCSINPNKKRSKKIKKLAKQKD IQACINIGNRYVDVPIRPVSVADPDTPKETKEDKEKGCHFRNGIH* >NC_001341.1_2 # 788 # 1009 # 1 # ID=1_2;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.306 MQCLISNEYHHNNNEHTSCINRINRNYRSNQRHHQGYNDLYDSINIIQGMLENLNASIVY FTKDGKYKLIMTL* Given this…

Putnam, N. H. et al. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317, 86–94 (2007). Article  ADS  CAS  PubMed  Google Scholar  Chapman, J. A. et al. The dynamic genome of Hydra. Nature 464, 592–596 (2010). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Srivastava, M….

•    2024 Toyota Corolla Cross: Here is pricing for the new year. Toyota brings virtually no changes to its Corolla Cross small SUV for 2024, the only modification worth mentioning being upgraded new 18-inch wheels for the LE Premium trim. Other than that, the offering remains the same, save for…

When compared to the genomes of other RNA viruses, coronaviruses have been found to possess largest genome sizes. They are capable of establishing reservoirs in both human and zoonotic populations, enabling their transmission and circulation among a range of animal hosts, including bats, pangolins, civets, cats, mice, pigs, whales, dogs,…

Rasche M, Zimmermann M, Borschel L, Bourquin J, Dworzak M, Klingebiel T, et al. Successes and challenges in the treatment of pediatric acute myeloid leukemia: a retrospective analysis of the AML-BFM trials from 1987 to 2012. Leukemia. 2018;32:2167–77. Article  PubMed  PubMed Central  Google Scholar  Manola KN. Cytogenetics of pediatric acute…

Identification of the AP2/ERF transcription factors in lettuce genome To identify AP2/ERF family genes in lettuce, we queried the lettuce genomic protein database (version 8) using the Pfam model (PF00847) of the AP2 domain. This search led us to discover 223 genes that showed a significant match with the AP2…

Zachos, J., Pagani, H., Sloan, L., Thomas, E. & Billups, K. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292, 686–693 (2001). Article  ADS  CAS  PubMed  Google Scholar  Favre, A. et al. The role of the uplift of the Qinghai-Tibetan Plateau for the evolution of Tibetan…

BLAST1 is widely used in molecular biology to search for nucleotide and protein sequences. Three decades after BLAST was introduced, there were major breakthroughs in structure prediction, and tools such as RoseTTAFold2 and AlphaFold3 emerged. Consequently, every protein sequence in the major sequence databases now comes with a model of…

Rouard, M. et al. Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana). Genome Biol. Evol. 10, 3129–3140 (2018). CAS  PubMed  PubMed Central  Google Scholar  Langhe, E. D., Vrydaghs, L., Maret, P. D., Perrier, X. & Denham, T. Why bananas matter: an introduction to the history…

1. Introduction Orientia tsutsugamushi (OT) is an obligate intracellular parasite bacteria and the causative agent of scrub typhus (ST), which is associated with acute febrile illness (AFI) [1] and transmitted by mites through an infected chigger bite (in the larval stage). This disease, which was earlier believed to be endemic…

Christmas at the Park organiser David Trim said it was great to see so many children having fun. Photo / Paul Taylor A crowd of 13,000 let their hair down after a rough year in Hawke’s Bay, leaving Christmas at the Park organisers delighted. Even the viability of the show…

Bark preparation Spruce bark was obtained from the Iggesund pulp and paper mill (Iggesund, Holmen AB, Sweden), from a bark pile resulting from stripping of spruce logs at the mill after harvest, with the average age of trees at harvest being ~70 years. The bark was left to dry at…

Names: Section # & Bench #: COMPLETE INDIVIDUALLY! Lab 11 – Bioinformatics & BLAST Lab 11 Assignment – BLAST reports (15 points) Due: By next week’s lab ● Complete this sheet, download as Word doc, submit on Canvas Activity 1 Report – BLAST 1. What is the name of the…

Jurassic Park DNA sequence &&)’A dinosaur sequence appears on page °±² of 20Jurassic Park³ by Michael ((+)Crichton ´”*(Ballantyne ”*(Books³ °$!$!²µ¶ 1/In it³ the 1/In,/-Gen’s chief scientist³ )),*Dr¶ -0.Henry Wu³ indicates that the sequence “probably contains instructions to make a single protein ·· say³ a hormone or an enzyme”¶ So what…

Bacterial strains We used P. putida strains S12, DOT-T1E, F1 (kindly gifted by Grant Rybnicky), ATCC 12633 (purchased from ATCC), JUb85 (kindly provided by Samuel Buck), EM383 (kindly gifted by Huseyin Tas), p106 (kindly provided by Carey-Ann Burnham), and KT2440 (obtained from lab stocks). An overnight culture of each P….

Keller, J. K. Wetlands and the global carbon cycle: what might the simulated past tell us about the future?. New Phytol. 192, 789–792 (2011). Article  CAS  PubMed  Google Scholar  Dolinar, N., Rudolf, M., Šraj, N. & Gaberščik, A. Environmental changes affect ecosystem services of the intermittent Lake Cerknica. Ecol. Complex….

LCA from BLAST output 1 I have a fairly large BLAST output from a metagenomics project with millions of lines per sample. The input sequences for the blast search were prodigal annotated proteins. I have been looking for a while now to find a suitable program that calculates the LCA…

How to avoid missannotated GO terms? 1 Hi, I am doing GO enrichment analysis for the newly annotated plant genome. I did BLAST against Swissprot plant proteins and extracted the GO IDs of matching hits. I observed that there are some miss annotated proteins, like the following: P04145 (Assigned GO…

ISCA fabrication VeroGray polymer was used to create 3D-printed moulds on an Objet30 3D printer (Stratasys), using previously described protocols32. Each ISCA consisted of 25 wells arranged in a 5 × 5 array. Each 110 µL well possessed a 800-μm-diameter port that connected the inside of the well with the surrounding seawater and…

The circular RNA (circRNA) circZBTB46 was expressed at increasing levels among patients with higher risk myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML) and was associated with shorter survival, according to the results of a study published in the journal Clinical and Experimental Medicine. A type of noncoding, stable RNA,…

Friedman-Einat, M. & Seroussi, E. Avian leptin: bird’s-eye view of the evolution of vertebrate energy-balance control. Trends Endocrinol. Metab. 30, 819–832 (2019). Article  CAS  PubMed  Google Scholar  International Chicken Genome Sequencing C. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695–716 (2004)….

Issues while running blastx 1 Hi, I face this problem when I run blastx command in linux. blastx -db ~/Downloads/uniprot_sprot.dat -query ../../../trinity_out_dir.Trinity.fasta -num_threads 2 -max_target_seqs 1 -outfmt 6 > balstx.outfmt6 Warning: [blastx] Examining 5 or more matches is recommended BLAST Database error: No alias or index file found for protein…

megablast taxonomy assign in blobtools 0 I made taxonomy assignment file using megablast and ran blobtools create, view, plot. However I couldn’t get any taxonmy assignment in the plot, there is only undefined. How can I get bacterial information ? $blastn -task megablast -db ${nrdb} -query scaffold$i.fa -outfmt ‘6 qseqid…

Study areas The samples were collected from wild boars hunted in rural properties from the municipalities of São Simão, Monte Azul, Paraíso, Colina, Matão, Bebedouro e Monte Alto (São Paulo), Ipiranga (Paraná), and Santo Antônio das Missões (Rio Grande do Sul) (Fig. 1). Fig. 1 Sampling collection sites of wild boars…

Batinovic, S. et al. Bacteriophages in natural and artificial environments. Pathogens 8, 100. doi.org/10.3390/pathogens8030100 (2019). Article  PubMed  PubMed Central  Google Scholar  Mushegian, A. R. Are there 10^31 virus particles on earth, or more, or fewer?. J. Bacteriol. 202(9), 2020. doi.org/10.1128/JB.00052-20 (2020). Article  Google Scholar  Kutter, E. & Sulakvelidze, A. Bacteriophages:…

Page not found at /GeneAnnotation/?id=Pzi006309&type=Pzijinensis Using the URLconf defined in orchidbase5.urls, Django tried these URL patterns, in this order: ^admin/ ^rec_histone/$ [name=”main_algorithm”] Info_download/$ [name=”Info_download”] Sum_download/$ [name=”Sum_download”] example_download/$ [name=”example_download”] ^ ^$ [name=”home2020″] ^ ^geneinfo2022/ [name=”geneinfo2020″] ^ ^releaseSummary2022/ [name=”releaseSummary2020″] ^ ^orchidSpecies/ [name=”orchidSpecies”] ^ ^Contacts/ [name=”Contacts”] ^ ^Orchidbase4.0_user_guide/ [name=”Orchidbase4_user_guide”] ^ ^Orchidbase5.0_user_guide/ [name=”Orchidbase5_user_guide”] ^…

Microbial gene coverage from blast result 0 Hello all I am new to BLAST and Biostars. I have removed human-mapped reads from RNA-Seq data and did Kraken2 and Bracken analysis using the microbial reads. Using the Kraken Tool, I retrieved the microbial reads. Then I performed BLASTx in order to…

Which region of the rRNA is used for synethsizing primers for species identification?5 answersThe region of the rRNA used for synthesizing primers for species identification is the mitochondrial 12S rRNA gene. This gene segment is commonly targeted in PCR-based methods for species identification and taxonomic classification. It has been used…

How to resolve the error of protein lacking a stop codon when using GenomeThreader for homology prediction? 0 Dear all,the error message and running process are as follows. Thank you for your answers. makeblastdb -in pudorinus.fa -parse_seqids -dbtype nucl -out index/pu& nohup tblastn -query all.pep.fa -out pu.blast -db index/pu -outfmt…

Hi, I’m using blastn in BLAST 2.11.0 and it keeps failing for specific sequences for a reason that I’m yet to understand. Any lead on what he problem might be? The error message is Error: NCBI C++ Exception: T0 “/tmp/BLAST/2.11.0/gompi-2020b/ncbi-blast-2.11.0+-src/c++/src/serial/objistrasnb.cpp”, line 499: Error: (CSerialException::eOverflow) byte 132: overflow error ( at…

Error in blast+ 0 Hello, I have a problem with creating a local database (blast+) I downloaded NCBI BLAST and then put a fasta file in the bin folder. Later I opened this folder in PowerShell and wrote a command “makeblastdb -in ownBLASTdb.fasta -out DataBase -dbtype prot -parse_seqids”. I got…

Centers for Disease Control and Prevention (U.S.). Antibiotic Resistance Threats in the United States, 2019. doi.org/10.15620/cdc:82532 (2019). Centers for Disease Control and Prevention. COVID-19: U.S. Impact on Antimicrobial Resistance, Special Report 2022. doi.org/10.15620/CDC:117915 (2022). Fricks-Lima, J. et al. Differences in biofilm formation and antimicrobial resistance of Pseudomonas aeruginosa isolated from…

Product Details Description: Anti-XRCC1 (CHICKEN) Antibody – 200-901-MG5 Synonyms: Chicken Anti-X-Ray Repair Cross Complementing 1 Antibody, X-Ray Repair Complementing Defective Repair In Chinese Hamster Cells 1, X-Ray Repair Cross-Complementing Protein 1, DNA Repair Protein XRCC1, SCAR26, RCC Host Species: Chicken Clonality: Polyclonal Format: IgY Target Details Gene Name: XRCC1  – View…

Plant material Five alfalfa plants (stems and leaves) were sampled from each of the four different fields, 10–15 acres in size, located in Yuma Country, Arizona, USA. Geographic coordinates of the alfalfa fields and the adjacent crops are shown in Table 1. Table 1 Geographic locations of alfalfa fields Total…

Loeb, V. et al. Effects of sea-ice extent and krill or salp dominance on the Antarctic food web. Nature 387, 897–900 (1997). Article  ADS  CAS  Google Scholar  Atkinson, A., Siegel, V., Pakhomov, E. & Rothery, P. Long-term decline in krill stock and increase in salps within the Southern Ocean. Nature…

Phylogenomic analysis of Orthopoxvirus genomes A phylogenomic analysis of 200 Orthopoxvirus genomes, identified 10 distinct clades within this genus, which are here named as phylogroups 1 to 10 and are denoted as OPV-PG-01 to OPV-PG-10 (Fig. 1) based on their nesting patterns (Supplementary Fig. S1), where the 100 MPV isolates included…

Viral metagenomic analysis The number of clean reads was 21,157,543 for the RNA sample and 26,789,502 for the DNA sample. For RNA, the data were assembled to a total sequence length of 2,337,534, with 60.92% GC content. The length of the largest contig was 11,556 nt, which was identified as…

Abstract The mitochondrial genome, mtDNA, is present in multiple copies in cells and encodes essential subunits of oxidative phosphorylation complexes. mtDNA levels have to change in response to metabolic demands and copy number alterations are implicated in various diseases. The mitochondrial HMG-box proteins Abf2 in yeast and TFAM in mammals…

Bioinformatics develops as a region of limitless possibility in the  science and technology, where biology converges with computing capability. Consider a future in which every strand of DNA contains the key to revolutionary discoveries and individualized therapy. Welcome to the dynamic world of Bioinformatics, a discipline that bridges conventional divides…

regarding blast result interpretation 1 How to interpret blast result for e.g., when I blast Gohir.D13G088900 in Arabidopsis thaliana i got mainly two results At1g62040 with e-value 1e-67, percent identity 88% and score 200 bits(508) 2.At2g05630 with e-value 2e-66, percent identity 92% and score 197 bits (500) out of these…

Hello, please help a struggling wet-lab biologist. I am trying to identify Cluster of Orthologous Groups (COG) categories for a list of gene sequences. I configured a COG database and used DIAMOND to blast query sequences against this database. This provides a results.cog file that in my case is formatted…

Hello ! I’m currently trying to develop a local core-genome MLST tool using a combination of a huge genes database and blastn but I came into outputs I can’t explain. Here’s what I have: My genome: genome.fasta My database, comprised of ~1000 genes and n alleles: db/GENE01.fasta: 1500 sequences. db/GENE02.fasta:…

Introduction Thiopurine S-methyltransferase (TPMT) is a cytoplasmic enzyme that catalyzes the S-methylation of purine analogs, including azathioprine, 6-mercaptopurine (6-MP), and thioguanine.1 The metabolism of these drugs results in two types of metabolites: S-methylmercaptopurine and S-methylthioguanine, which are generally described as inactive metabolites, and S-methyl-thioinosine monophosphate, an inhibitor of de novo…

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410 CrossRef  CAS  PubMed  Google Scholar  Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database…

Barnett R. Schistosomiasis. (1474–547X (Electronic)). Steinmann P, Keiser J, Bos R, Tanner M, Utzinger J. Schistosomiasis and water resources development: systematic review, meta-analysis, and estimates of people at risk. Lancet Infect Dis. 2006;6(7):411–25. Article  PubMed  Google Scholar  Uthailak N, Adisakwattana P, Thiangtrongjit T, Limpanont Y, Chusongsang P, Chusongsang Y, et…

Rowe RG, Daley GQ. Induced pluripotent stem cells in disease modelling and drug discovery. Nat Rev Genet. 2019;20:377–88. Article  CAS  PubMed  PubMed Central  Google Scholar  Li L, Papadopoulos V. Advances in stem cell research for the treatment of primary hypogonadism. Nat Rev Urol. 2021;18:487–507. Article  CAS  PubMed  Google Scholar  Lawrence…

Inhibition effect of strain SH-1471 on plant pathogenic fungi The results of the plate confrontation experiment showed that B. velezensis SH-1471 had good inhibitory effects on various pathogenic microorganisms (Fig. 1). Specifically, our experiment showed that its inhibition rates on Sclerotinia scrotiorum, Phoma mateuciicola, and Fusarium oxysporum were 93.5%, 90.3%, and…

The difference blastn output when using subject and db options 0 I have blasted the candidate transposable element to my genome. When I use (db) command 1 (details below) then the output is small and different from the command 2 using subject parameter with same query . If anybody has…

Adékambi T, Drancourt M, Raoult D (2009) The rpoB gene as a tool for clinical microbiologists. Trends Microbiol 17:37–45 CrossRef  PubMed  Google Scholar  Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410 CrossRef  CAS  PubMed  Google Scholar  Arahal DR,…

Transcribed image text: In regards to bacterial DNA and sequencing, answer the following Statements as True or False: About 95% of DNA is identical among different species of bacteria. Looking at the different sequences will identify specific species. After sequencing, we use the BLAST computer database to identify the bacterial…

Hi Biostars, I am currently trying to build a Eukaryote version of the NCBI NR database and I am not really sure that I fully understand how the NR is implemented. Here is the code that I’m using to do so : #!/usr/bin/bash ############## # DOWNLOAD FULL NR ############## baseURL=”https://ftp.ncbi.nlm.nih.gov/blast/db/”…

BLAST, or Basic Local Alignment Search Tool, is a powerful and widely used bioinformatics tool for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotide sequences of DNA. The main purpose of BLAST is to identify sequences in a database that are similar…

Analyzing genomic data, from sequences to structures, is a critical aspect of bioinformatics. Python has a rich ecosystem of tools and libraries specifically designed for genomic data analysis. Here’s an overview of key tools and libraries for various stages of genomic data analysis: Description: Biopython is a comprehensive open-source collection…

Biopython is an open-source collection of Python tools for computational biology and bioinformatics. It provides modules and classes to work with biological data such as DNA, RNA, protein sequences, structures, and more. Biopython aims to make it easy for developers to access and manipulate biological data in a programmatic way….

Genome sequencing and assembly of R. tetraphylla After DNA extraction from young leaves and sequencing, the R. tetraphylla genome was first assembled into 1008 contigs with an N50 of 3.7 Mb. After haplotigs removal and a final pilon polishing, the 364,945,498 bp final assembly was distributed across 76 scaffolds with an N50…

Afridi MS, Amna S et al (2019) Induction of tolerance to salinity in wheat genotypes by plant growth promoting endophytes: Involvement of ACC deaminase and antioxidant enzymes. Plnat Physiol Biochem 139:569–577. doi.org/10.1016/j.plaphy.2019.03.041 Article  CAS  Google Scholar  Ali S, Charles TC, Glick BR (2014) Amelioration of high salinity stress damage by…

Plasmid construction All the constructs used in this study were generated with standard cloning strategies, including PCR, overlapping PCR, oligo annealing, digestion and ligation. Primers were purchased from Genewiz. The plasmid sequence was verified by Sanger sequencing. The pCAG-spike(D614G)-GFP11-mCherry plasmid was modified from Addgene plasmid 158761. Briefly, GFP11 and mCherry…

BLAST hits on viruses relate to different host than used 0 Hey guys, I have just recently (9 days ago) posted about metagenomic analysis of phages. I hope it is okay, to post again right now, the issue is different this time. I am struggling a bit with deciding which…

Soltis, D. E. et al. Polyploidy and angiosperm diversification. Am. J. Bot. 96, 336–348 (2009). Article  PubMed  Google Scholar  Van de Peer, Y., Mizrachi, E. & Marchal, K. The evolutionary significance of polyploidy. Nat. Rev. Genet. 18, 411–424 (2017). Article  PubMed  Google Scholar  Amborella Genome Project et al. The Amborella…

Tool:SEDA (SEquence DAtaset builder): a desktop tool for processing FASTA files containing DNA and protein sequences 4 Dear community members, We present SEDA, an open source application for processing FASTA files containing DNA and protein sequences. The source code is available at GitHub and a complete user manual is available…

Introduction The development of multicellular organisms requires the activation of different gene batteries which specify the identity of each individual cell type. Such shifts in cellular identity are driven by shifts in the gene regulatory network (GRN) consisting of transcription factors (TFs) binding to the enhancers and promoters of their…

Cat# I7663-31L-APC-100ul Size : 100ul Brand : US Biological Host mouse Conjugate APC Isotype IgG1 Clone Number 10B1132 (IL-A111) Grade Affinity Purified Applications IHC IP Shipping Temp Blue Ice Storage Temp 4°C Do Not Freeze Applications: Suitable for use in Immunohistochemistry, Immunoprecipitation and Functional Assays. Other applications not tested. Recommended…

Cat# I7663-31L1-100ug Size : 100ug Brand : US Biological Host mouse Conjugate FITC Isotype IgG1 Clone Number 10B1132 (IL-A111) Grade Affinity Purified Applications FC Shipping Temp Blue Ice Storage Temp -20°C The CD25 cell surface antigen is a 55kDa glycoprotein also known as Interleukin-2 receptor alpha chain. Bovine CD25 is…

Tripp, H. J. et al. SAR11 marine bacteria require exogenous reduced sulphur for growth. Nature 452, 741–744 (2008). Article  ADS  CAS  PubMed  Google Scholar  Yu, X. J., Walker, D. H., Liu, Y. & Zhang, L. Amino acid biosynthesis deficiency in bacteria associated with human and animal hosts. Infect. Genet. Evol….

Affiliations Expand Affiliations 1 Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, Barcelona, Catalonia, Spain. 2 ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain. 3 Department of Clinical Sciences, Faculty of Medicine and Health Sciences and Universitat de Barcelona Institute…

News:NCBI BLAST+ 2.2.15 now available for download 0 BLAST+ 2.2.15 is now available. The new release can run multithreaded searches faster and can focus your searches by organism groups more easily. Automatic threading model switchingBLAST+ can now run 2-10x faster for small databases and large numbers of queries when you…

Introduction The CRISPR-Cas system is a widely used genome engineering technology because of its simple programmability, versatile scalability, and targeting efficiency (Wang & Doudna, 2023). Although researchers are rapidly developing CRISPR-Cas9 tools, the biggest challenge remains to overcome undesired on- and off-targeting outcomes. Previous studies have reported unintended genomic alterations,…

Blood samples, DNA extraction, mitochondrial genome amplification and sequencing Following established procedures, bat blood samples were collected from designated sampling sites in Kanchanaburi, located in western Thailand, during the years 2019 and 202123,33,34. For this study, four bat samples (2 Myotis siligoensis and 2 Hipposideros gentilis) were utilized. These samples…

Genome length and GC content Using a hybrid approach that combines Oxford Nanopore long reads and Illumina short reads data, we assembled a scaffold-level version of Ae. koreicus and Ae. japonicus genomes whose size was assessed as 1.24 and 1.39 gigabase (Gb) pairs, respectively. These dimensions resemble those of other…

SnapGene viewer information for DNA sequence data Download free version of SnapGene Viewer. Do NOT sign up for ‘free’ trial full version as after 1 month you then need to pay and you do NOT need full version. snapgene/snapgene-viewer/ Pick the version for PC or Mac and one which fits…

Cat# I7663-31L-AP-100ul Size : 100ul Brand : US Biological Host mouse Conjugate AP Isotype IgG1 Clone Number 10B1132 (IL-A111) Grade Affinity Purified Applications IHC IP Shipping Temp Blue Ice Storage Temp 4°C Do Not Freeze Applications: Suitable for use in Immunohistochemistry, Immunoprecipitation and Functional Assays. Other applications not tested. Recommended…

Ethics statement All mice procedures in this study were performed under an animal protocol approved by the Institutional Animal Care and Use Committee guidelines of Westlake University. The procedures and protocols for glioma patients were approved by the institutional review board of Beijing Tiantan Hospital. Informed consent was obtained from…