Any tool to generate protein similarity matrix
Hi, I want to calculate the similarities between each protein pariwise and then implement random walk to predict interactions. A paper mentions "J. Mol. Biol. (1981) 147, 195-197" to compare two...
View ArticleProblem With Blastp Of Biopython: Returned Non-Zero Exit Status 1
I want to do a local BLAST using blastp from the Bio.Blast.Applications. However, when I run it I get a runtime error: returned non-zero exit status 1. According to the manual it is Exit Code Meaning:...
View ArticleHow To Show More Blast Results Using Biopython?
Hi,I'm using biopython to BLAST over the internet. However, it only saves 30 results (there are more than 30 results that are under the e-value I chose) in the xml. I've been looking all over but can't...
View ArticleMost Sensitive Method To Search 100-1000Bp Sequences To Genome At Human-Mouse...
Following up on this question: http://biostar.stackexchange.com/questions/8010/searching-200-400bp-matches-against-mammalian-genome-human-mouse-distance I would like to know what is the most sensitive...
View ArticleHow Can I Sort Blast Output Based On E-Value?
Hello: I have a blast output with about 50000 sequence list. The problem I have is that I need to sort those results based on the smallest e-value to greater e-value. Could you guys please suggest me...
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 ArticleBiojava And Blast+
Dear all, i´m currently trying to parse several blast output files in order to show the results in my software. Since i have to carry out many blast searches from time to time, i decided to install the...
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 ArticleHow To Automate Primer Blast With Perl?
Hey all!does any one have a PERL script for automating the PRIMER BLAST tool.... i.e. i want a script which will submit my fasta file and parameters to Primer BLAST and retrieve the output. I'm stuck...
View ArticleDownload Ensembl Blastn Result
Hi,How can I download blast results from ensembl. I blast 10 sequences against all ensembl species. Now I have the result page and I want to download all hits to compare them.Is it possible ?Here's the...
View ArticleHelp With Rps-Blast With New Blast
HiI want to make rpsblast with the new blast 2.2.25 with rpstblastn. But I need to format the database. I think for the older blast version you use formatrpsdb and it´s create others files including...
View ArticleBLAST in Oracle 12c
Hello dear colleagues,BLASTN_MATCH and other BLAST alignments were available in Oracle 10g in Oracle Data Mining (ODM) package.Is there BLAST in 12c?If not, is there a way to install BLAST from 10g to...
View ArticleComparing Blast M8 Outputs
Hi,I want to compare BLAST outputs in m8 format to find out if any queries in the separate output files have the same subject hits to NCBI nr database.For example, for the 2 BLAST outputs in m8 format...
View ArticleHow to create a Blast database of viruses ?
Hi all,For a metagenomic project a want to make a blast database of viruses. I dont want to blast my reads on the entire nt database. But I dont know how to make it. Downloading the result of a query...
View ArticleBLASTP many pairs of peptide sequences
Dear all,I have many pairs of protein sequences, an example shown below.MDDDIAALVVDNGSGMCKAG DDDIAALVDNSGSMCKAGTTAEREIVRDIKEKLCY TTAEIVRKEKLCYVARMQKEITAPSTMKIKI KEITALPSTMKIKII... ...I need to...
View ArticleAre old versions of NCBI's nr stored somewhere?
Hello,I'd like to study how NCBI's non-redundant protein database (nr) has developed over the years. However, I'm yet to find a way to download anything but the latest release from the NCBI ftp. Are...
View ArticleHow To Get Blast+ (Stand Alone Blast) Output To Contain Only The First Hit...
Greetings! I'm using BLAST+ v. 2.2.26, and would like to customize the output to include only the FIRST hit for each separate record in the data base. The region I am using as the query is a domain...
View ArticleBlast Two Sequences
Hello all! I have a list of pairs of proteins and I want to compare speed and accuracy of "BLAST Two Sequences" to a Smith-Waterman program for alignment. I know there is a "Blast Two Sequences" option...
View Articlerecruitment plot - blast output
Hello Guys,Does anyone have a tutorial for generating recruitment plot from a file output blast? thanks!
View ArticleBlast+ Stand Alone Version For Sequence Alignment
HiOn the on line version of Blastp (link text) there is a sequence alignment section (and it produces E-values for the alignment).and now I want to use the standalone version to perform alignment(My...
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