How Is The Word Score For The Look-Up Table Determined For Blast?
I'm going over some slides about BLAST from an introductory course of bioinformatics. I don't understand how the words for the look-up table are scored. The query sequence is split up in words of 3...
View ArticleHow To Find Paralogs Using Blast
I am trying to find paralogous genes in a model organism (Arabidopsis). To do that am using blast with the sequence for its own database. The first hit I get is the protein sequence aligned with it...
View ArticleDefault Frameshift Penalty For Blastx
I do not set the frameshift penalty costs and output everything in BLAST XML format. Then I go through this file and usually the beginning contains parameters of the scoring scheme etc. But it does not...
View ArticleSearching 200-400Bp Matches Against Mammalian Genome (~Human-Mouse Distance)
Hi,What would be a good tool to use to query 200-400bp intergenic sequences from one mammalian species to the reference genome of another, something like human-mouse distance? Blast?Just to clarify, I...
View ArticleProblem Running Blast Jobs.
I started to run blast, locally on my machine, on 4 files with 1323, 210, 501, 166 fasta sequences each.For all jobs except the first one blast returned an error:blastall(7004) malloc: ***...
View ArticleAnnotating Sequences For Gbrowse - Which Is The Database And Which Is The Query?
Let's say I have some small sequences that I wish to display in Gbrowse. I want to create tracks from Blast results to show where genic regions might be.Do I create a Blast index of the small sequences...
View ArticleBlast Output Into Jsp/Html
I would like to display a blast result in a jsp or html by parsing the xml result of blast without using BioJava? how can I do that?
View ArticleMakeblast Db Problem
I try to get makeblastdb working on windows. I installed blast-2.2.23-ia32-win32 . I followed the tutorial at http://www.mesb.bse.vt.edu/publications/Stand%20alone%20BLAST%20simple%20tutorial.txtI put...
View Articlencbi-blast warning: Selenocysteine (U) at position ** replaced by X
Hi all, I just want to know what does this warning message means.There's a way to suppress blast+ warings? The old blast has a flag -warnings as parameter, but the blast+ doesn't.
View ArticleHow To Prove An Ortholog Does Not Exist In A Given Genome?
I am wondering what is the best way to prove that an ortholog is absent (or at least un-identifiable) from a given sequenced genome.My initial thought goes to a tblastx search, where an absence of...
View ArticleRun Multiple Sequences Through Psipred
Hi, I have psipred working (thanks to some posters on here) and can confirm it works for single sequences - however when I input a fasta file with multiple sequences it only gives the output for the...
View ArticleIs Matching Blastn Output A Requirement For Alternative Sequence Matching...
I've read a paper demonstrating an implementation of sequence alignment and the authors indicate that in order to provide substantial speed gains they must compromise on query size and output fidelity,...
View ArticleProblems With Biopython When Running The Ncbistandalone.Py Program
Hi, I am having problem while running NCBIStandalone library of biopython. i want to retrieve sequence titles from output of blast but it gives error on iterator. Following is the code to retrieve...
View ArticlePsiblast: Stop After Checkpoint?
Hi,I'm using psiblast 2.2.25+ to generate PSSMs for PSIPred, and I noticed that even after writing to the checkpoint file, it takes a while (feels like half the run time) before exiting, even though I...
View ArticleNcbi Wgs/Nt/Env-Nt Databases
I am currently BLASTning against NCBI's NT database but I am considering also using WGS and ENV-NT. I was given the impression that WGS was populated by pulling from ENV-NT if the sequence was...
View ArticleCan Bio.Blast.NCBIXML somehow parse the stdout from NcbipsiblastCommandline...
Hi, I would like parse the XML output of a local psiblast (NcbipsiblastCommandline wrapper) by putting the stdout from the wrapper into a python string variable and then using NCBIXML.parse to parse...
View ArticleDistribution of e-values in Best Reciprocal Blast Hits for Ortholog Mining
Does anyone have an idea of how the distribution of expect values will look when using reciprocal blast to detect orthologs?
View ArticleFinding Coordinates Of Genes In Genome
Hi GuysI think I have a very trivial question. I have a multi-fasta file of rRNA genes. I need to find their location in the genome. It will be easy to blast them but not sure how can I extract the...
View ArticleLooking For Frequency Of A Very Specific Rna Editing Event In Publicly...
I am working on a ubiquitously and well expressed gene whose ~1.5 kb-sized transcripts get mutated at one and only one site. The mutation is a nonsense one that changes an ORF codon of the mRNA to a...
View ArticleSequence Blast Against Rfam Database
Hi All,I am using blastn to blast my data against tRNAs which is extracted from RFam database. Then I picked one match from the blast result to confirm it by directly searching my read in RFam online...
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