Script to detect mismatches and indels in BLAST report
Hi!I am trying to find antibiotic resistant reads in 454 metagenomic datasets. The problem is that resistance against certain antibiotics e.g. fluoroquinolones and rifampin is conferred though...
View ArticleBlastn - Program Runs Indefinitely When Generating Xml Formatted Output
I am running blastn on some nucleotide data, and it seems to run indefinitely when I generate XML output. The jobs take ~15 minutes when generating either the default format or tab delimited, but when...
View ArticleHow To Translate Old Parameters In New Version Of Blast 2.2.27 +
Hi, I am a beginner in blast. I can't figure out how to write options for the new version of blasts. I read manuals, but it confused me more.How to translate this options for new version of blast-F "m...
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 ArticleErrors In A Bioperl Script, Please Help Me To Have A Check, Thanks In Advance!
Dear friends: I have a blast report, and want to extract following information for each result(query): the Query_name, hit_number, name and description of the hit(HSP) with the highest identity. my...
View ArticleBlast Result Matching Both Of Two Query Sequences?
If two short sequences (A and B) come from the same gene, but I don't know the name of the gene or the organism, can I perform a BLAST (or similar) search to find the gene which has best similarity...
View ArticleHave You Ever Tried Megablast Indexation ?
Hi, I am surprised to see as low number of posts about megablast indexing... Is this because it does not work? If I believe this one, this should really help to get results faster. But after some...
View ArticleAre The Query Strand And Hit Strand From Blastx The Same Strand?
I'm writing code to parse the XML output from a BLASTX search on NCBI's servers, and from this grab from NCBI the nucleotide sequence whose translated protein was found to be a hit by BLASTX . This is...
View ArticleSetting E-Value In Blast
Hi,Again I realize that its an easy question :). Could anyone tell me how to set e-value to 0.005 in Blastp?
View ArticleBlast Contigs To A Reference Sequence And Obtain An E-Value
Well, I'm a newbie of blast, so...hope I'm not asking a stupid question....I've already have a set of contigs which is done by de novo assembler. Format of these contigs is fasta. Now I want to align...
View ArticleObtaining the top matches from blast
Hi,I have downloaded the current version of the stand-alone-blast (ncbi-blast-2.2.29+) and I am trying to use blast (blastn) to find similarity of of a group of nucleotide sequences that I have....
View ArticleQuery Vs. Target Using Blast2
I'm running blast2 locally using DNA sequences in fasta files. I have one large target and a load of smaller query sequences.Version: 1.2.2.21.20090809-1 (blast2)blast2 -p blastn -r 0 -q -2 -G 2 -E 2...
View ArticleHow Long Should It Take To Make A Blast Database?
HiI'm trying to install a local copy of polyphen and one of the stages is to make a blastdb from uniref100.I ran this command last night and its still going nearly 12 hours later. I don't know if this...
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 ArticleDetecting Derived Sites
I am working on coding sequences of two plant species and have identified their orthologs using reciprocal best BLAST hits. For detecting the derived site in one of the species (of interest) I am...
View ArticleBlast Execution Problem
Hi, I am trying to have the command line blast work, however, I did not manage to execute it properly. I would appreciate if you can tell me what I am doing wrong. So here are the things I did so far:...
View ArticleHow Can I Save A Blast Record (.Xml) Into A Suitable Format For Excel (.Xls)?
I have made a BLAST search through the NCBIWWW.qblast command in Biopython. After having my results saved in a .xml format (by result_handle way, following Biopython tutorial chapter 7) I have parsed...
View ArticleBlast: Homology Or Similarity?
Hi Biostars, I am having a dispute with a reviewer. Is BLAST a Homology or similarity based search? thanks EDIT The BLAST is performed against a custom DB containing only homologous proteins.
View ArticleWhat Is The Lowest E-Value In Blast When Ncbi Rounds It Down To 0 (Zero)?
Hello, Just out of curiosity, an E-value of more significant hits in BLAST approach 0, but cannot equal 0. In some cases when the E-value of a HSP is very low NCBI BLAST rounds it down to 0. What is...
View ArticleJava Equivalent Of Biopython'S Ncbixml Parser
I'm looking for a method similar to Biopython's parse method of NCBIXML in javathis is the parse methodhttp://biopython.org/DIST/docs/api/Bio.Blast.NCBIXML-module.html#parse
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