Tag: BLAST

Yu, Z., Loisel, J., Brosseau, D. P., Beilman, D. W. & Hunt, S. J. Global peatland dynamics since the Last Glacial Maximum. Geophys. Res. Lett. 37, L13402 (2010). van Breemen, N. How Sphagnum bogs down other plants. Trends Ecol. Evol. 10, 270–275 (1995). Article  Google Scholar  Johnson, M. G. et…

New species account Taxonomy: Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Scolioidea; Scoliidae; Scoliinae, sensu Raznitsyn27; Campsomerini; Dielis Saussure & Sichel, 186428. Dielis tejensis sp. nov. urn:lsid:zoobank.org:act:7E4E00DB-180B-427A-886A-13FB4DF53F6D. Habitus: Fig. 1, Supplementary Fig. S1. Figure 1 D. tejensis sp. nov. and its mitochondrial genome. Open arrows indicate the location of…

Andersen LO, Bonde I, Nielsen HB, Stensvold CR. A retrospective metagenomics approach to studying Blastocystis. FEMS Microbiol Ecol. 2015. doi.org/10.1093/femsec/fiv072. Article  Google Scholar  Audebert C, Even G, Cian A, Loywick A, Merlin S, Viscogliosi E, et al. Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human…

Luo, M. C. et al. Synteny analysis in rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials. BMC Genom. 16, 707 (2015). Article  Google Scholar  Martinez-Garcia, P. J. et al. The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of…

Orcutt B, D’Angelo T, Jungbluth SP, Huber JA, Sylvan JB. Microbial life in oceanic crust. OSF Preprints, 2020; doi.org/10.31219/osf.io/2wxe6. Koonin EV. On the origin of cells and viruses: primordial virus world scenario. Ann NY Acad Sci. 2009;1178:47–64. Nigro OD, Jungbluth SP, Lin HT, Hsieh CC, Miranda JA, Schvarcz CR, et…

Introduction Proteases regulate various biological processes including protein synthesis and maturation, activity modification, degradation and turnover. Depending on their catalytic mechanisms, these proteases are primarily classified into cysteine, metallo-, serine, threonine and aspartic protease family (Beers et al., 2004). The latter protease family is known as acid protease family because they…

Isolation of M. synoviae field isolates M. synoviae field isolates were obtained from approximately ninety flocks of registered commercial chicken farms, including breeder flocks, broiler flocks, and layer flocks in Thailand in 2020. Chickens were individually swabbed at the articular joint or the respiratory tract; choanal cleft, tra,chea and airsac;…

which tool to use for Transposon structure finding CENSOR or repeat masker ?? 0 I have a nucleotide sequence as a query. I need to align the respective organisms’ reference genomes and identify if there is an inverted repeat around the query and genome-mapped sequence. I have seen some papers…

According to Levinthal’s paradox, each protein may adopt around 10300 distinct structures. We now know 3-D structures for about 98% of the human proteome thanks to DeepMind’s AI system, AlphaFold. However, AlphaFold has limitations, such as its inability to generate coordinates for tiny molecules and ligands that are critical to…

Viral metagenomics is the study of viruses in environmental and biological samples by utilizing next generation sequencing that generates very large data sets. Viral metagenomics analyzes viral sequences to deduce the impact of viruses on the environment of human health. Unlike amplicon sequencing, metagenomics obtains and investigates genetic material directly…

Animals As female mice/rats resist to HFD-induced obesity and NAFLD, male mice/rats were used to induce obesity and NAFLD model by HFD50. Male Wistar (~180 g body weight; 8 weeks old) rats were purchased from Shandong Laboratory Animal Center with the permission number of SCXK 2014–0007 and raised under thermoneutral housing…

blastn (Error: Too many positional arguments (1)) 1 Hello, I want to use blastn to search a particular query in the fasta format ($QUERY) I’ve created database from each .fna file using `”makeblastdb -in $GENOME -dbtype nucl -parse_seqids” (for different purposes, I run also blastcmd which runs normally without any…

Isolation, phenotypic identification, pathogenicity and antibiogram profiling Enterococcus faecalis strains BFF1B1, BFFF11 and BFPS6 were cultured in Streptococcus selective agar media (Himedia, India). The culture characteristics such as colony, morphological, physiological and biochemical characteristics of these strains BFF1B1, BFFF11 and BFPS6 were summarized in the Supplementary Table S1. All of…

When an underwater volcano erupted in 2015 it created a new island as the Hunga Tonga Hunga Ha’apai island emerged from the ocean. It would live fast and die young with just a seven-year lifespan from emergence to submergence, but in those short few years, a team of scientists had…

NCBI DB and Taxonomy classification 1 Hi, I’d like to perform a taxonomic classification (not only of microorganisms but also of all Eukaryota) of shotgun output sequences with megan6, which requires to download a reference db with sequences or genomes to compare. I was looking for something usefull in the…

EMBOSS: dbxflat dbxflat   Function Index a flat file database using b+tree indices Description dbxflat indexes a flat file database of one or more files, and builds EMBOSS B+tree format index files. These indexes allow access of flat files larger than 2Gb. Usage Here is a sample session with dbxflat…

Papillomaviruses are non-enveloped, double-stranded DNA (dsDNA) viruses with a circular genome. Infection with these viruses can lead to several clinical symptoms ranging from subclinical, cutaneous, and mucosal warts to cancerous lesions in vertebrate hosts.  A new study published in the journal Biology Letters identifies two novel lineages of papillomaviruses by mining…

Hall, B. K. & Wake, M. H. in The Origin and Evolution of Larval Forms (eds Hall, B. K. & Wake, M. H.) 1–19 (Academic Press, 1999). Nielsen, C. Animal phylogeny in the light of the trochaea theory. Biol. J. Linn. Soc. 25, 243–299 (2008). Article  Google Scholar  Garstang, W….

Introduction Clostridioides difficile (C. difficile) is an anaerobic, gram-positive, spore-forming bacillus and important pathogen of antimicrobial-associated diarrhea and nosocomial diarrhea in humans.1 Clostridioides difficile infection (CDI) can progress from self-resolving diarrhea to colitis, life-threatening pseudomembranous colitis and toxic megacolon, and death.2,3 CDI is a toxin-mediated disease, and the major virulence…

Biopython vs Python Hi, Please help – If already have python 3 in laptop, is biopython still needed to download? I already downloaded python 3; when I checked on the www.bippython.org, there is also “download”, are they the same or different? sorry if it is a naive question. Thank you…

How to do typing of VDJ regions for10x TCR kit? 2 I am analyzing the full-length sequencing of TCRs or precisely VDJ regions. Although I worked in the NGS field for some time,” immunoinformatics ” is new to me. How to do the typing for VDJ. It is not in…

Pfeffer C, Larsen S, Song J, Dong M, Besenbacher F, Meyer RL, et al. Filamentous bacteria transport electrons over centimetre distances. Nature. 2012;491:218–21. Article  CAS  Google Scholar  Lovley DR, Holmes DE. Electromicrobiology: the ecophysiology of phylogenetically diverse electroactive microorganisms. Nat Rev Microbiol. 2022;20:5–19. Article  CAS  Google Scholar  Bjerg JT, Boschker…

Downloading NT chunks from NCBI and creating a BLAST database 0 Hello, everyone! This is my first post on this blog. I’ve been attempting to write Python code to download every nt chunk from NCBI (ftp.ncbi.nlm.nih.gov/blast/db/) (nt.00.tar.gz, nt.01.tar.gz, etc) and their md5 files (nr.00.tar.gz.md5) and extract them all within a…

Tool for aligning short protein sequences 2 Hi, I have a file that looks like: >ref_frame=1 XFKKNLAFLQKKAKEFSSEQTRANSPTRRELQVWGRDNNSPSEA >ref_frame=2 FLKKIWPSYKKRPKNFLQSRPEPTAPPEESFRSGVETTTPPQKQ >ref_frame=3 F*KKSGLPTKKGQRIFFRADQSQQPHQKRASGLG*RQQLPLRSR >read1_frame=1 FFKKNLAFLQKKAKEFSSEQTRANSPTRRELQVWGRDNNSPSEA >read1_frame=2 FLKKIWPSYKKRPKNFLQSRPEPTAPPEESFRSGVETTTPPQKQ >read1_frame=3 F*KKSGLPTKKGQRIFFRADQSQQPHQKRASGLG*RQQLPLRSR I want to do a protein alignment where I align each read frame against each ref frame. What tool can I use to…

how to output blastx results with full accession 1 Hello All, I am running blastx with my assembled transcriptome against a local database, which was built from a fasta file. The fasta file contains protein sequences with long accession names. e.g. >tr|A0A1P8ASE7|A0A1P8ASE7_ARATH Cold-shock protein OS=Arabidopsis thaliana OX=3702 GN=AT1G34049 PE=4 SV=1…

1Department of Pediatrics, Affiliated Hospital of Weifang Medical University, Weifang, People’s Republic of China; 2Department of Dermatology, Affiliated Hospital of Weifang Medical University, Weifang, People’s Republic of China Correspondence: Weiyuan Ma, Department of Dermatology, Affiliated Hospital of Weifang Medical University, Weifang, People’s Republic of China, Tel +86-536-3081272, Email [email protected] Yongfeng…

Materials Medakamo hakoo 311 was obtained from the personal aquarium of Prof. Kuroiwa (Kagurazaka, Tokyo, Japan)4. The M. hakoo strain was cultured in 0.05% HYPONeX (HYPONeX Japan Corp., Ltd., Osaka, Japan) liquid medium and on 0.05% HYPONeX gellan gum-based solid medium in plates. Cyanidioschyzon merolae 10D (Toda et al. 1995)…

Data collection Metagenomic project information was collected from the MGnify metagenomic database31. Currently (September 2021), microbiome data (sequence, taxonomic, and functional information, etc.) of 325,323 environmental samples can be found in this database. Often, microbes from similar ecological communities have been studied by different groups at different times and locations….

makeblastdb next generation suite of BLAST sequence search tools Maintainer: Debian Med Packaging Team Section: science Install makeblastdb Debian apt-get install ncbi-blast+ Click to copy Ubuntu apt-get install ncbi-blast+ Click to copy Kali Linux apt-get install ncbi-blast+ Click to copy Fedora dnf install ncbi-blast+ Click to copy Raspbian apt-get install…

Blanco-Fernandez, C. et al. Fraud in highly appreciated fish detected from DNA in Europe may undermine the development goal of sustainable fishing in Africa. Sci. Rep. 11, 11423. doi.org/10.1038/s41598-021-91020-w (2021). Article  ADS  CAS  Google Scholar  Lewis, S. G. & Boyle, M. The expanding role of traceability in seafood: Tools and…

accession DB alignment Evalue Score Ident. link information pubmed 1 Q55221_STRSQ(Q55221) 1e-146 522   100% Product Polyketide reductase Gene dauB Organism Streptomyces sp 1uniprot[Pubmed] 7928998 [Medline] 95014072 Isolation and sequence analysis of polyketide synthase genes from the daunomycin-producing Streptomyces sp. strain C5.(J. Bacteriol.) [1994] 2 Q54812_STRPE(Q54812) 1e-129 466   90% Product Daunorubicin-doxorubicin…

First molecular identification of A. putorii in China The mt cox1 sequence of PCR amplicon of 652 bp (GenBank accession no: OP363931) using primer pair JB3-JB4.5 as previously described [21] showed only 81.7% identities to GenBank no. MH665361 by BLAST search, which was a Capillaria sp. This low identity indicates the…

Eisenstein, M. Big data: the power of petabytes. Nature 527, S2–S4 (2015). Article  CAS  Google Scholar  Trewavas, A. A brief history of systems biology: ‘Every object that biology studies is a system of systems’. Francois Jacob (1974). Plant Cell 18, 2420–2430 (2006). Article  CAS  Google Scholar  Dixon, S. J., Costanzo,…

Bioinformatics Alignment/Map (BAM) is a powerful tool used to analyze and compare biological sequences. BAM is used to identify genetic variations, detect structural rearrangements, and compare different genomes. It is an essential tool for many areas of bioinformatics, including genomics, proteomics, and transcriptomics. In this article, we will discuss 10…

Background: The Basic Local Alignment Search Tool (BLAST) is a suite of commonly used algorithms for identifying matches between biological sequences. The user supplies a database file and query file of sequences for BLAST to find identical sequences between the two. The typical millions of database and query sequences make…

Blastn Segmentation Fault 4 Hi, I am running a BLASTN of about 150 sequences against a genome that is 2.2 gigabases long. A few of my queries are actually full length BAC end sequences running to around 150,000 bases. I expect to find huge, contiguous hits for some BACs in…

HHS Vulnerability Disclosure, Help This document is an overview of the Entrez databases, with general information on If you are not sure that the “Save” option in your program will do this for you, use “Save As”, In Excel, select “Save As” from the File menu. optimizations to reduce memory…

Discovery of 11 new Cas12a candidates from a human gut microbiome database To discover new members of the Cas12a protein family, we built a pipeline that searches and sorts out new candidates from the National Center for Biotechnological Information (NCBI) human metagenome database. Using this search pipeline (Fig. 1a), we initially…

Isolation, characterization and classification of BC-producing strain Isolation of single clones from CaCO3 halo zones in Glucose-Yeast Extract-Calcium carbonate agar and iterated subculturing in HS-Glu agar resulted in enrichment of an isolate with beige-coloured, smooth-edged and umbonate shaped colonies characteristics (Fig. S1A). The isolate is hereafter called ‘ENS15’. Under 100X magnification,…

Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, et al. A new view of the tree of life. Nat Microbiol. 2016;1:16048. Article  PubMed  Google Scholar  Castelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT, Wilkins MJ, et al. Genomic expansion of domain archaea highlights roles…

BLASTP – Searching for homologous sequences of small peptides in several species 0 Hello! I now have some protein sequences of a number of species (chicken, human, mouse, …). I want to use BLASTP to find the homologous sequence of a small peptide “KPWLRVALCPG” in these species. For the convenience…

Kegg orthology is a database of genes with known identity and function. You can submit genomic data to be referenced against that database. I love using kegg to produce genome summaries such as what metabolic pathways are complete and incomplete, and what percentage of genes in the genome are dedicated…

Sample collection Colobanthus quitensis samples were collected at King George Island near the Henryk Arctowski Polish Antarctic Station, Maritime Antarctica (62°14’ S, 58°48’ W) during the summer season (February 2018). Samples were collected inside the Antarctic Specially Protected Area (ASPA) 128 using permits provided by The Chilean Antarctic Institute (INACH)…

Ethics statement All procedures involving laboratory mice were approved by the Duke University IACUC under the protocol numbers A189-18-08 and A142-21-07. Mice were housed with up to five mice per cage and the ambient room conditions ranged from 70–74 °F and 30–70% humidity with a 12-hour dark/light cycle. Animals were assessed…

Genomic features of two Anastatus wasps, A. japonicus and A. fulloi We employed PacBio high-fidelity (HiFi) long-read sequencing and Illumina short-read sequencing technologies to generate high-quality contigs for two Anastatus wasps, A. japonicus and A. fulloi (Supplementary Tables 1 and 2). These contigs were further scaffolded using Hi-C libraries to…

The Job Dispatcher service at the EMBL-EBI provides access to various sequence analysis tools and a database retrieval system (Dbfetch). This virtual course is split into two sessions running over two days.  During the first session, you will learn how to access and use our sequence…

Smid, E. J. et al. Practical implications of the microbial group construction of undefined mesophilic starter cultures. Microb. Cell Factories 13, S2. doi.org/10.1186/1475-2859-13-S1-S2 (2014). Article  Google Scholar  Stadhouders, J. & Leenders, G. J. M. Spontaneously developed mixed-strain cheese starters. Their behaviour in direction of phages and their use within the…

Overview of the viromes In all, 41 wild Qinghai voles were collected from pasture habitats located on the eastern Tibetan Plateau, China (Fig. 1). Tissue samples from liver, lung, spleen, small intestine (with content), and feces (large intestinal content) of each vole were disrupted, and viral RNA was extracted. The RNA…

Organisation of the Pregap4 Manual Introduction Summary of the Files used and the Processing Steps Introduction to the Pregap4 User Interface Introduction to the Files to Process Window Introduction to the Configure Modules Window Introduction to the Textual Output Window Introduction to Running Pregap4 Pregap4 Menus Pregap4 File menu Pregap4…

I got fasta output by using the following codes in R. And I need to read my fasta file (homo_ref.faa) that I obtained using these codes as “ makeblastdb -in homo_ref.faa -dbtype prot ” via terminal. But I get “BLAST options error: File homo_ref.faa does not exist“. How would you…

Merlino, C. P. Bartolomeo Bizio’s letter to the most eminent priest, Angelo Bellani, concerning the phenomenon of the red-colored polenta [translated from the Italian]. J. Bacteriol. 9, 527–543 (1924). Grimont, P. A. D. & Dulong de Rosnay, H. L. C. Numerical study of 60 strains of Serratia. J. Gen. Microbiol….

Gengis Don & The Empire collide two musical worlds and leave their funky fingerprints on the music as the audience joins along a journey through the Hip Hop universe. Blast off in 3, 2, 1…described as the love child of Jazz & Boom Bap, Gengis Don has a sound of his own….

BLAST unmapped reads from BAM 0 Hey, I have sequenced a recombinant plasmid and I am trying to characterize the insert sequences that have not aligned to the reference. I have generated a BAM file with the unmapped sequences and now I am trying to BLAST these in various databases…

blast ring image generator PROBLEM 0 Good day or evening, in search of a working program for visualizing the complete genome, tried to use BRIG, but instead of the result we got (see fig1) nothing, some one now what the hell ?. I tried to compare 4 genomes of chlamydia…

Sampling the radiation To understand the phylogenetic relationships between Alpine whitefish, we carried out whole-genome resequencing on 96 previously collected whitefish (with associated phenotypic measurements including standard length and gill-raker counts; collected in accordance with permits issued by the cantons of Zurich (ZH128/15), Bern (BE68/15), and Lucerne (LU04/14); these fish…

Cui, B., Smooker, P. M., Rouch, D. A., Daley, A. J. & Deighton, M. A. Differences between two clinical Staphylococcus capitis subspecies as revealed by biofilm, antibiotic resistance, and pulsed-field gel electrophoresis profiling. J. Clin. Microbiol. 51, 9–14 (2013). CAS  PubMed  PubMed Central  Article  Google Scholar  Tevell, S., Hellmark, B.,…

How to replace underscore between digits and character or at second place (_) in protein seq header & discriptions 1 Hi, I want to remove(_) sign between the accession number and their description name like this -> ALKAOGAL_00001 Chromosomal_replication_initiator_protein_DnaA in all protein seq. Is there any script for this please…

Salje, J. Cells within cells: Rickettsiales and the obligate intracellular bacterial lifestyle. Nat. Rev. Microbiol. 19, 375–390 (2021). CAS  PubMed  Article  Google Scholar  Wang, S. & Luo, H. Dating Alphaproteobacteria evolution with eukaryotic fossils. Nat. Commun. 12, 3324 (2021). CAS  PubMed  PubMed Central  Article  Google Scholar  Strassert, J. F. H.,…

Mokomane M, Kasvosve I, Melo Ed, Pernica JM, Goldfarb DM. The global problem of childhood diarrhoeal diseases: emerging strategies in prevention and management. Ther Adv Infect Dis. 2018;5(1):29–43. PubMed  Google Scholar  Organization WH. Rotavirus vaccines: WHO position paper–July 2021. Weekly Epidemiol Rec. 2021;96(28):301–219. Google Scholar  Bucardo F, Reyes Y, Svensson…

Zaremba-Niedzwiedzka, K. et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353–358 (2017). CAS  PubMed  Article  Google Scholar  Williams, T. A., Cox, C. J., Foster, P. G., Szöllősi, G. J. & Embley, T. M. Phylogenomics provides robust support for a two-domains tree of life. Nat. Ecol….

Name Last modified Size Description Parent Directory   –   Aligned_Reads/ 2016-07-30 04:38 –   Cufflinks_Output/ 2017-11-11 11:53 –   FEELnc/ 2018-08-14 16:03 –   Gene_Expression/ 2016-09-01 14:14 –   Genome/ 2018-04-04 15:54 –   Intermediate_LncRNA.feelncclassifier.log 2016-08-05 15:59 18K   LncRNA/ 2018-08-08 11:07 –   Raw_Reads/ 2016-07-28 15:11 –  …

doi: 10.1016/j.fm.2022.104043. Epub 2022 Apr 23. Affiliations Expand Affiliations 1 Department of Food Science and Technology, The University of Georgia, 1109 Experiment Street, Griffin, GA, 30223-1797, USA. 2 Department of Food Science and Technology, The University of Georgia, 1109 Experiment Street, Griffin, GA, 30223-1797, USA. Electronic address: jchen@uga.edu. Item in…

Since 2010, there have been multiple new species added to the Listeria genus, many originally isolated from natural environments16. This paper describes the genotypic and phenotypic characterization of two new Listeria isolates obtained from soil samples collected in the Great Smoky Mountains National Park along the North Carolina-Tennessee border17. Evaluation…

BlastX through Biopython 0 I have an unknown gene segment in the Human_gene.txt file and I want to run blastx (translated nucleotide) using the blast module of Biopython by making the E-value threshold 0.0001 and displaying the match result of 50 residues of query and subject. I am trying this…

Article, 2014 In: Journal of Bioinformatics and Sequence Analysis, ISSN 2141-2464, Volume 6, 1, Pages 1-6, 2014 DOI:10.5897/ijbc2013.0086 Organisations Abstract Following advances in DNA and protein sequencing, the application of computational approaches in analysing biological data has become a very important aspect of biology. Evaluating similarities between biological sequences…

Hello everyone I have multiple short sequences of SARS-COV-2 in the range of 500-800 nucleotides, I need to blast them, I get a good result on BLAST-NCBI, but is there anyone here who uses AudacityInstant which belongs to GISAID, this site aligns only sequences higher than 10000 nucleotides, as you…

the FASTA format is not “officially” defined – even though it carries the majority of data information onliving systems. Its origins go back to asoftware tool calledFastawritten byDavidLipman(ascientist that later became, and still is, the director of NCBI) andWilliam R. Pearsonof the University ofVirginia. The tool itself has (to some…

BenchSci’s vision is to bring novel medicine to patients 50% faster by 2025. We’re achieving it by empowering scientists with the world’s most advanced biomedical artificial intelligence. Backed by F-Prime, Gradient Ventures (Google’s AI fund), and Inovia Capital, our platform accelerates science at 15 top-20 pharmaceutical companies and over 4,300…

What you are trying to do is fairly simple, and you are complicating it by: 1) not providing your sequences so that someone can reproduce your attempt; 2) giving a result in a form that is impossible to read. Be honest, can you make any sense of the result you…

Hey guys Self hit I have this actually a bit weird question about blast. I’ve been doing some work around single copy genome construction using Reciprocal best blast hit (RBBH) method. As I have something like 100+ annotated genome, I concatenated all annotated CDS into one fasta and makeblastdb with…

Conda recipes for the bioconda channel. 4571 Projects Similar to Bioconda Recipes Sequenceserver Intuitive local web frontend for the BLAST bioinformatics tool Homebrew Bio 🍺🔬 Bioinformatics formulae for the Homebrew package manager (macOS and Linux) Galaxy Data intensive science for everyone. Travel Guide “A travel guide to suggest activities you…

Provided by: libbio-perl-perl_1.7.2-2_all NAME Bio::Tools::Seg – parse “seg” output SYNOPSIS use Bio::Tools::Seg; my $parser = Bio::Tools::Seg->(-file => ‘seg.fasta’); while ( my $f = $parser->next_result ) { if ($f->score < 1.5) { print $f->location->to_FTstring, ” is low complexity\n”; } } DESCRIPTION “seg” identifies low-complexity regions on a protein sequence. It is…

Qiime2 Exclude Seqs with FASTQ as query data. 0 Hello, I am working with FASTQ files and I want to filter them based on the alignment with references sequences in FASTA format. I decided to use QIIME2 for this. So I imported both FASTA and FASTQ files to the required…

Eddykay310 Hi @cruizperez Please help me understand the problem here and how I can fix it. I have successfully generated my DBs but I get this error during analysis. The .dmnd files do not exist in the folders as the error says but I don’t know how I can generate…

Hi all, I’m trying to create a local nt blast database, my eventual goal is to create a subset based on a taxanomic group to be used on a cluster with limited storage space, its seems the only way to do this though is to start with the whole database…

Does anyone know? how to sort one16s rDNA from multiple 16s rDNA in one strains for phylogenetic tree construction? 3 Hi, i had extract 16srDNA sequence by using barrnap from complete genome of each strains. These are the output which are given below. Actually when i opened each strains file…

Share Tweet Share Share Email ClustalW is a computer tool of significant importance in bioinformatics. Primarily, biologists and statisticians used it for multiple sequence alignment. Many versions of ClustalW over the development of the algorithm are available now. How to perform a search on ClustalW? ClustalW homepage 1. Go to…

Introduction Escherichia coli is a common Gram-negative opportunistic pathogen that causes invasive host infections through virulence factors such as flagella, toxin secretion, and adhesins. According to the source of the infection, pathogenic E. coli can be classified as intestinal (diarrheagenic) and extraintestinal (ExPEC). Uropathogenic E. coli (UPEC) is the most…

In Chapter 2 we learned how to search databases with text queries. All of these were exact matches—that is, we were expecting to find the exact accession number or exactly spelled words. In this chapter, a much harder database-searching problem is introduced. How do you find matches when your query…

BLASTn using R 0 Hello, I have around 2000 DNA nucleotide sequences (60 bases long) stored in each row in an excel sheet. I want to run BLAST over each one of them individually and extract the “Description” of the first hit. Like for Example: Suppose on NCBI BLAST website…

Biopython NcbiblastpCommandline not working: “No such file or directory: ‘test.xml” 0 from Bio.Blast.Applications import NcbiblastpCommandline blastp=r”C:\NCBI\blast-BLAST_VERSION+\bin\blastp.exe” blastp_cline = NcbiblastpCommandline(blastp, query=r”C:/NCBI/blast-BLAST_VERSION+/bin/test.fasta”, db=r’C:/NCBI/blast-BLAST_VERSION+/bin/bos_protein.fasta’, outfmt=5, evalue=0.00001, out=r”C:/NCBI/blast-BLAST_VERSION+/bin/test.XML”) blastp_cline from Bio.Blast import NCBIXML with open(“test.XML”) as result_handle: E_VALUE_THRESH=0.01 blast_records = NCBIXML.parse(result_handle) blast_record = NCBIXML.read(result_handle) for alignment in blast_record.alignments: for hsp in alignment.hsps: if hsp.expect…

Methods The study was conducted at the Human Genetics Unit, Faculty of Medicine, University of Colombo. It was an experimental study, where a novel assay was designed for the targeted variant, and a cohort of hormone receptor positive breast cancer patients were genotyped for the CYP2D6*10 variant using the optimized…

Introduction The study of the microbial environments has benefited from the sequencing revolution, where technology improvement decreased the DNA sequencing cost and increased the number of sequenced nucleic bases. For approximately 20 years (depending on how we define the term metagenomics), it has allowed the decryption of the microbial composition…

How can I find genes located in the same region (overlapping) of the chromosome ? 1 I take the BAM file as input and perform RNA-Seq. The program prints out a list of genes to which the reads match. Some of the genes in the list overlapping in the same…

From scientific name to taxonomy information entrez 1 Hi all, I have a txt file with a list of scientific names of plants and I would like to obtain a final file with taxonomy information. For example, if one of my organism is Acalypha hispida, I would like to obtain…

Source: www.nature.com/articles/s41587-021-01179-w.epdf Proteins play an important part in the construction and function of all living organisms. Each protein is made up of a chain of amino acid building blocks. Much like an image might have numerous things, a protein can have multiple components, known as protein domains. Researchers have been…

Name Last modified Size Description Parent Directory   –   nextorf.py 2010-10-07 10:28 9.1K   test.fas 2010-10-07 10:28 517   testrp.fas 2010-10-07 10:28 50K   xbb_blast.py 2010-10-07 10:28 4.7K   xbb_blastbg.py 2010-10-07 10:28 2.3K   xbb_help.py 2010-10-07 10:28 2.2K   xbb_search.py 2010-10-07 10:28 5.0K   xbb_sequence.py 2010-10-07 10:28 399  …

Wu, W. et al. NDM metallo-β-lactamases and their bacterial producers in health care settings. Clin. Microbiol. Rev. 32, e00115–18 (2019). Yong, D. et al. Characterization of a new metallo-β-lactamase gene, bla NDM-1, and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14…

We implemented a metagenomic DNA sequencing methodology to unbiasedly detect microbial species in CSF samples from patients with CNS symptoms in which a pathogen or EBV had been detected (Additional 3: Table 1). Samples positively identified with pathogen-specific quantitative PCR (qPCR), 16S rRNA gene sequencing or bacterial/mycotic culture in CSF…

DOI: 10.18129/B9.bioc.TAPseq     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see TAPseq. Targeted scRNA-seq primer design for TAP-seq Bioconductor version: 3.12 Design primers for targeted single-cell RNA-seq used by TAP-seq. Create sequence templates for target gene panels and design gene-specific primers using…

I’m trying to blastp multiple aminoacids sequences using biopython. I just can’t seem to get it right and i cant figure out the handbook for how to do this. I have come up with the following: open(“proteins_PROT.fasta”,”r”) from Bio.Blast.Applications import NcbiblastpCommandline cline = NcbiblastpCommandline(query=”proteins_PROT.fasta”, db=”nr”, evalue=0.001, remote=True, ungapped=True) NcbiblastpCommandline(cmd=’blastp’, query=”proteins_PROT.fasta”,…

Associated RNAi Experiments Homology BLAST of peroxisomal multifunctional enzyme type 2-like vs. L. salmonis genes Match: EMLSAG00000010112 (supercontig:LSalAtl2s:LSalAtl2s668:190059:194758:1 gene:EMLSAG00000010112 transcript:EMLSAT00000010112 description:”augustus_masked-LSalAtl2s668-processed-gene-1.1″) HSP 1 Score: 102.064 bits (253), Expect = 2.195e-25Identity = 65/191 (34.03%), Postives = 101/191 (52.88%), Query Frame = 0 Query: 134 GKVALVTGAGGGLGKAYALLLASRGASVVVNDLGGSRTGEGQSSKAADEVVNEIRQKGGKAV—–GNYDSVEDGEAVIKTALDNFGRIDIVINNAGILRDRSIGRTSDSDWDLVQKVHLRGAFQVIRAAWPHMKKQKYGRIINTSSVAGIFGNFGQSNYSSAKAGLIGLTSTLAIEGERSGIQANVIVP 319 GKVAL+TGA G+G++ A+L A…

INTRODUCTION Next-generation sequencing (NGS) has revolutionized many areas of biological research (1, 2), providing ever-more data at an ever-decreasing cost. One such area is microbiome research, the study of microbes in their theater of activity using metagenomic sequencing (3). Here, deep short-read sequencing, and improving performance of long-read sequencing, are…

The taxonomy of the genus Neisseria remains confusing, particularly regarding Neisseria mucosa and Neisseria sicca. In 2012, ribosomal multi-locus sequence typing reclassified both as N. mucosa, but data concerning 17 N. sicca strains remain available in GenBank. The continuous progress of high-throughput sequencing has facilitated ready accessibility of whole-genome data,…

Although the hypothesis of gene-regulatory network (GRN) cooption is a plausible model to explain the origin of morphological novelties (1), there has been limited empirical evidence to show that this mechanism led to the origin of any novel trait. Several hypotheses have been proposed for the origin of butterfly eyespots,…

M. Madan Babus Group and the Center for Data-Driven Discovery in the Department of Structural Biology is seeking a highly driven, Full time Machine Learning Research Scientist support the Kalodimos and Babu Groups on the Blue Sky Initiative “Seeing the Invisible in Protein Kinases.” This project is supported by $35…

Errors /blast/moderated Leave a mail with to get this resolved. Contact: VIB / UGentBioinformatics & Evolutionary GenomicsTechnologiepark 927B-9052 GentBELGIUM+32 (0) 9 33 13807 (phone)+32 (0) 9 33 13809 (fax) Don’t hesitate to contact the in case of problems with the website! You are visiting an outdated page of the BEG/Van…

Serratus alignment architecture Serratus (v0.3.0) (github.com/ababaian/serratus) is an open-source cloud-infrastructure designed for ultra-high-throughput sequence alignment against a query sequence or pangenome (Extended Data Fig. 1). Serratus compute costs are dependent on search parameters (expanded discussion available: github.com/ababaian/serratus/wiki/pangenome_design). The nucleotide vertebrate viral pangenome search (bowtie2, database size: 79.8 MB) reached processing rates…

I recently had a script fail due to poor handling of BLAST output. The BLAST -outfmt staxids field usually returns a single taxid, but occasionally it returns two or more taxids separated by a semicolon, such as 556514;701533. Fixing the script to handle this should be fairly straightforward. But the…

News:NCBI looking for testers for a new web-only (for now) clustered `nr` database 0 Find details about how to participate by going to this link. Clustered nr is the standard NCBI nr database clustered with each sequence within 90% identity and 90% length to other members of the cluster. Your…