Blast Search Implementation In Biojava
Hello!I would like to write the BLAST Search algorithm using BioJava for a school project.I can not find any sources, tutorials, nothing in the BioJava Cookbook. I would like to specify the query and...
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 ArticleLimit The Memory Size Of Blast?
Would anyone tell me whether it is possible to limit the memory size in blast+/blastall search? If possible, how should we do it? Thanks!
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 Is The Score And E-Value Calculated In Blast Outputs
Hi!I am working on a BLAST similar tool and wanted to implement the Score (raw Alignment score) and the E-value. I was wondering if someone could please explain me how it is calculated by showing it...
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 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...
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Is the source code for the NCBI-BLAST service available anywhere?
Hello!Is the source code for the NCBI-BLAST service available anywhere? In particular, I'm interested in producing the visualization NCBI-BLAST offers, such as the one below, using BLAST results from...
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 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,...
View ArticleHow to understand which DNA strand is (5' to 3' ot 3' to 5') in the result of...
Hi!if a have such a result from a blast run, how can i understand if its in the 5' or 3' side of the DNA or protein strand ?> gnl|SRA|SRR456295.4505.2 FIHSSUW02H237H.2 length=250 Length=250 Score =...
View ArticleBest Hits From Blast Tabular Output Of Multiple-Queries
Hello. I have been trying to get the best hits out of blast output files. I know that -v option or maxtargetseqs in standalone blast gives the best ones. But I already have a huge output of multiple...
View ArticleBlastp And Tblastx Bitscores
I am using BLAST 2.2.25+ command line version with default penalties. I have a set of nucleotide sequences. I manually did a 6 frame translation with BioPython and blastp the 6 frames to NR protein....
View Articleconverting a fasta database to blastp database
hello im runnnig a wwwblast software on my server i do have a fasta database and i would like to use it in wwwblast i googled it a little and found that " makeblastdb " does the job i used this command...
View ArticleStrange Behaviour Of Bioperl'S Bio::Searchio When Parsing Xml Blast Output
Hello, I've noticed some strange behaviour when parsing BLAST .xml output files (-oufmt 5) using BioPerl's Bio::SearchIO library. I have a simple parser script that looks something like:...
View ArticleHow To Cluster Sequences Based On Blast Results?
I want to cluster a set of DNA sequences into families based on BLAST results. Is there any idea what software I can use to do it? Thanks!
View ArticleHow To Blast A Nucleotide Profile (Pssm) Against A Nucleotide Database?
I saw that tblastn is capable of doing that kind of search, but I want my position-specific scoring matrix (pssm) to be built from nucleotide, not protein, sequences.Has anyone done something similar...
View ArticleIndividual Hit Gene Information From Qblast Xml Output
I've just started using Biopython, and I am trying to perform remote BLAST operations using the qblast() function. Everything seems to be working properly, but I am not being able to retrieve an...
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 ArticleHow To Examine Whether Homology Search Method Used(Blast/Hmmer) Is Feasible...
Hallo...how to one examine whether homology method used is feasible for identification of a particular gene family e.g HSP. Suppose i have identified 550 sequences suspected to be a particular gene...
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