Can I Have Blast Return One Hit Per Species
Hello all, I've been long troubled with redundant blast hits from different strains of the same species, for example, E. coli. These hits (can be dozens to hundreds) mask hits from other species which...
View ArticleStandalone Blast Options
Hi all , I'm using local BLAST to retreive the single top most hit invoking "-v" option of blastall/RPSBLAST, from the local database sequences. I'm getting the top hit in most of the cases but in some...
View ArticleAssigning subject to query based on coverage from blast output file
Dear all, I have blast result in tabulated format. Each of the query hits multiple subject sequences. From all of those hits, I want to assign that subject sequence which covers the query sequence the...
View ArticlePerl Script To Check Top Blast Hits
I search for a perl script to check if the top BLAST hits to a query contained a full scientific binomial, i.e. for see if the next best hit has a complete scientific name with taxonomy, and to sorted...
View ArticleDatabase Error When Running Blastn
Hello, as initially stated here, I am experiencing problems when I try to run the blastn command blastn -query myquery -db mydatabase.fasta.nhr.What I get is:BLAST Database error: No alias or index...
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 ArticleTurn Off Blast Search On Reverse Complement Strand In Blastn
I have a quick question: How can I turn off search on reverse complement strand of my query nucleotide sequence in blastn?For example, I don't want 'GUAAAGCCAAAUCUUCGGUUA' to be a hit when I use...
View ArticleVertebrate Subset Nr Database? Build My Own?
I think I have the answer to my own question, but I'm somewhat new to bioinformatics, and I want to make sure my strategy is sound (and that there are no easier solutions to my problem). We need to...
View ArticleWhy Do Blastall And Blast+ (Blastn) Give Different Results For What I Beleive...
I've recently run two searches, one with blastall (from legacy blast) and one with modern blastn. Both versions are 2.2.25 (the most recent).The blastall search is: blastall -i test.fasta -p blastn -d...
View ArticleMegablast, Makembindex, And Choosing Nmers
I've been using MegaBLAST (in BLAST+) to test for high-similarity matches against hg18. It's exponentially faster than normal blastn for this purpose, but I'm not sure what settings I should use when...
View ArticleWays To Quantify Proteome Analysis Via Blast
I'm working on software to allow users to blast an entire proteome against a manually curated database in order to attempt to quantify the composition of that organisms proteins against our database....
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 ArticleBl2Seq In Blast+
I have recently installed blast 2.2.24+ and I was looking for the bl2seq tool, but I didnt find it. After some research I found that bl2seq is only found in the legacy blast package. So my question is...
View ArticleIs Blast+ Running As Fast As It Could ?
Hi all, I am trying to run a tblastn search of nt locally using blast+2.2.25, and was wondering if anyone new if it's going as fast as it should - I have 1000's of queries to get through! I should...
View ArticleBlast: Influence Of Database Filesize On Performance, And Purpose Of...
Obviously BLAST is going to have better on-average performance on a smaller database than on a larger database. But for a particular (large) database (let's say 10s of GB), how does splitting up the...
View ArticleTaking Only Aligned Sequences In A Blast
Hello,I would like to know how to take (in FASTA format) only the sequences displayed as results of a BLAST, avoiding to search the desired sequences in the whole subjects' reports.
View ArticleBlast Query Against Two Different Taxa
Hi,I have a protein sequence which I first do a blastp against NR database without any limitations. It returns a possible protein family and an organism in the output with a very low E-value (something...
View ArticleNCBI BLAST+ installation problems?
Hello,I recently tried installing BLAST+ command line (I downloaded the .dmg application and the ncbi-blast-2.2.29+ folder) and tried running a blastn command in terminal, giving the following error:...
View ArticleStandalone BLAST with kingdom classification
Hi all,I have an assembled transcriptome from an organism hosting various symbionts and I'm now interested in how many of my contigs hitting to the different kingdoms. What I've found so far is the...
View ArticleParse Web Blast Output
I have installed NCBI wwwblast at our local server and blast is running absolutely fine. I wanted to refine the html output which the blast is showing. For example, while showing alignment description,...
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