Forum: How To Correctly Speed Up Blast Using Num_Threads
Hello, I did a short blast comparison using multiple cores to see how they behave. I published it in my blog and thought it would be a good idea to share it...
View ArticleBest Way To Grab All Ncbi Protein Sequences For A Specific Taxonomic Query?
I would like to retrieve all of the NCBI protein sequences that belong to a specific taxonomic query, or children of that query. For example, I want to get every protein sequence belonging to the...
View ArticleHow To Get Conservation Of Vaccine Candidates Between Hundreds Of Bacterial...
Hi community,We have identified vaccine candidates via an ex-vivo RNA-seq approach. Next step would be to perform conservation of these candidates (about 20) between multiple bacterial strains (about...
View ArticleBlastclust Output Problem.
HI,I have installed the blast standalone latest version 2.2.25 with the help of the installation guide http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/pc_setup.html. I ran the blast with a 14Mb fasta file...
View ArticleHelp With Formatdb And Blast All
I have my own database of sequences stored in MySQL. I convert this database into a blastable format using formatdb, code below:formatdb -p T -i db.fastaI then do the same with the query sequence and...
View ArticleBlast Xml Document Iterations
When running BLAST with one sequence against a sequence database there is only one iteration in the <Iteration> element, as in the value of Iteration_iter-num is one. For example:<?xml...
View ArticleLimit The Memory Size Of Blast?
Would anyone tell me whether it is possible to limit the memory size in blast+/blastall search? If possible, how should we do it? Thanks!
View ArticleI Use Blastdbcmd Command With Nr Database And It Gives Me The "Not Found...
This is the errorBLAST Database error: No alias or index file found for nucleotide database [nr] in search path [/home/aj3/Desktop/h/database::]what should I do? do I have to use any other commands...
View ArticleGet Query Coverage From Local Blast
Hi allDoes anyone have an idea how I can get the query coverage of my hits from local BLAST (in unix). The -m 8 option gives you a tabular output that does not contain the 'Descriptions' part of the...
View ArticleHow Can I Determine Whether Two Proteins Have The Same Multi Domain...
How can I determine whether two proteins have the same multi domain architecture? For example, if I do a BLAST search for proteins with high alignment scores, what can I do with the resulting list of...
View ArticleNcbi Refseq Viral Genomes
I want to create custom blastdb with all viruses available in the refseq. But I don't know which source files to use. My first point is:ftp://ftp.ncbi.nih.gov/genomes/Viruses/From research I concluded...
View ArticleBlast To Cytoscape
Hi Guys, I am trying to view the results of an all vs all blastp of some sequences with cytoscape. I've been using the Blast2SimilarityGraph app to read in my data (blast -m 8 + fasta file) and then a...
View ArticleHow Set A Pssm (Position Specific Scoring Matrix) When Querying With Blast+?
help me out if anyone knows the answer for my question, How to search a nucleotide database using PSSM ( i developed the PSSM using set of protein sequences from query set) Do provide me the command in...
View ArticleBlast Output With Species Name
Dear all,my question is very simple. I have reads from a human RNASeq and I would like to check for contamination on a specific virus family. So my pipeline looks like1) Align on the human genome...
View ArticleAssessing Quality And Accuracy Of De Novo Genome Assembly
All, I am curious whether anyone out there has a method for assessing the quality and accuracy of de novo genome assemblies? I am currently doing in silico simulations of de novo genome assembly from a...
View ArticleNcbi Standalone Blast -Outfmt
Hi,I want to include the % of query coverage in my standalone blast result. Can anyone help me with this ??RegardsBHARAT
View ArticleFind All Similar Sequences In Genbank
Hi, I would like to get a feel for how many sequences related to my virus of interest are available on GenBank. I am thinking about using a recursive BLAST approach. Start with one genome, BLASTn, and...
View ArticleHow I Can Find The Sequence For The Gene That I Want To Synthesize?
Hi,I'm starting with bioinformatic, and i want ask u this question:I have this sequence: vpnvrgmgar davylmekrg ikvritgrgr vieqslapgd kikngmqcsl rlg from "penicillin-binding protein dimerization domain...
View ArticleDoes Ncbitblastncommandline Reads The Outfmt (Options 6, 7, And 10 ) Correctly?
I am trying to call tblastn_hits = NcbitblastnCommandline(cmd='tblastn', query=query_handle, db=db_handle, num_threads=6, evalue=0.001, outfmt="6 qstart qend evalue bitscore", dbsize=10000000,...
View ArticleHelp With Bioperl Remote Blast Script (Bio::Tools::Run::Remoteblast)
Hi, I would like to run a blast search for a fasta file containing many (100+) seqences. I wrote a test script and ran it using a test query file (contains only one sequence; fh= diffexp1). If my code...
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