Blast Can'T Find Databases
I've installed BLAST locally, I've downloaded the nr database via update update_blastdb, I've added .ncbirc to the home folder which has [BLAST] BLASTDB=/home/bioinformatics/Desktop/blastDBand yet when...
View ArticleBlastn On Gpu?
Does anybody has an experience in running blastn (nucleotide sequence search) on GPU? The freely and easily obtainable tools only provide blastp that is for proteins. I need nucleotide search. As the...
View ArticleParsing Blast Results For Different Genus
Dear All,I have obtained several .gb BLAST results that I want to split in different .gb or .fasta files accordingly to genus.I searched for different ways to do it in the web, but didn't find a way to...
View ArticleScript To Submit And Manage Blast Jobs On A Cluster?
Hi,I make use of a local cluster (managed through LSF) to BLAST large sequence sets. I wrote a basic script to split a fasta file and submit each part as a different BLAST job. Does anyone know of such...
View ArticleDifferent blast results between CLCBio and local blast
Hi,I've been using CLCBio to blast assembled contigs, but it's really slow. I decided to try setting up a local blast database and using that to blast my contigs, but I'm getting different results even...
View ArticleHow To Produce An Analysis Report From Blast Output ?
Hello, is there a tool for processing the blast output and perform a statistical analysis of the alignment? For example a plot of the position of the mismatches? I cant believe that there is no...
View ArticleParsing Blast Output Biopython Error
Hi, I have the following code def runBLAST(self): print "Running BLAST .........." cmd=subprocess.Popen("blastp -db nr -query repeat.txt -out out.faa -evalue 0.001 -gapopen 11 -gapextend 1 -matrix...
View ArticleShowing Queries With No Hit In Tabbed Blast Output?
Hi, I was wondering if anyone could tell me if there's a way to get the tabbed BLAST output to show if there's not hit. I don't mind using either blastall or blast+.The reason I ask is that I'm trying...
View ArticleChanging evalue doesn't change the results of blast
Hi! First's run results occurred by this command : tblastn -query query.fasta -db plant_DB -out output-evalue -html and in some reads i got two targets. e.g : Score = 160 bits (404), Expect = 1e-44,...
View ArticleCompare Two Protein Sequences Using Local Blast
Hi,I have been given a task to compare the all the protein sequences of a strain of campylobacter with a strain of E.coli. I would like to do this locally using Biopython and the inbuilt Blast tools....
View ArticleE-Value In Blast
Hi all:I am calculating my e-Value for my own BLAST alignment. I used the formulae: e= mn2^-S'where: m = length of the query sequence n = total number of lengths of all template sequences in the...
View ArticleHow to analyze the ProDom output? I have some results to support the...
Hi all, I have some results retrieved from ProDom database and I need to analyze the output from 3 inputs to check if they share the same conserved domains, the results points to same description of...
View ArticleRun A Blast Daemon
I want to run my own BLAST daemon to avoid loading my blast db into RAM for every query.When I google it: I get a page from IBM that is out-of-date and a lot of other pages about Buffy the Vampire...
View ArticleBy What Criterion Can We Screen The Blast Results?
I used to select the first several sequences as the ideal sequences I want to get. But there are cases that a lot of sequences with high scores and low evalues will retrieve after blasting. When it...
View ArticleBLAST alignment score analysis
I've been evaluating a Smith Waterman implementation with ncbi BLAST and found out that for the same alignment (with no gaps) the alignment scores differ between those two algorithms. Here is the...
View ArticleProblems With Blast And Nr Database
I'm familiar with the BLAST family of software: I've used both the old interface (blastall, formatdb, et al) and the new interface (blastx, makeblastdb, et al). However, I've always used it with...
View ArticleHow To Use Blast To Find Exact Matches Of Short Sequences?
Hi, I am using tblastn (under blast 2.2.25+) for exact peptide mapping (no gaps). I want to map few peptides (about 6 to 50 AAs in length) to genome. However, as I test a known peptide of 6 AAs,tblastn...
View ArticleUsage Of Format Specifiers For Blastx In Ncbi Standalone Blast
Hi to all I am doing blastx with ncbi standalone blast for large number of sequences. I am getting the output in outfmt -7 (tabular with comment lines). There are 'keywords' like frames/qframe/sframe...
View ArticleHow Can I Get Older Versions Of Psi-Blast Program?
Hi,Do you know how I can get older versions of PSI-BLAST.Right now, I've downloaded 2.2.26, but I need to use these parameters. (Pardon me for the irrelevants). blastpgp -i seq-file -Q...
View Articleerror downloading refseq for local BLAST install via FTP
I am having trouble downloading the refseq database required for BLAST+. I am following the instructions from http://www.ncbi.nlm.nih.gov/books/NBK52640/ but get No such file or Directory error using...
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