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Questions tagged [blast]

BLAST is a Basic Local Alignment Search Tool for comparing biological sequence information.

Given some query string, it finds similar (although not necessarily identical) biological sequence strings in a large set of possible candidates. BLAST supports searches with possible sequence mismatches, deletions and insertions. BLAST is open source, written in C++, and was originally developed in 1990.

Wikipedia summary

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what is the meaning of multiple HSPs under a single hit?

I am new to the field of Bioinformatics. I was looking at a BLAST xml output file and I was trying to understand why there are multiple HSPs under each blast hit. I know HSP stands for High-Scoring Segment Pair but I don't really understand how and…
user3208598
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perl script to select best blast gene line from blast result

I have huge file with blast output and I need to select the query ID, subject gi and the frame (basically the whole line) with lowest e-value omitting the duplicate lines (omitting all other lines with other higher e-values). This is how the file…
user3171118
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The system() of Perl "paused". Caused by $ARGV[]?

I was stuck when combining the BLAST command into perl script. The problem is that the command line paused when the PART II begin. PART I is used to crop the fasta sequence. PART II is used to do BLAST with the file generated by PART I. Both the two…
Young_Bioinfo
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how to replace the same number of file1 with same number from file2

i have a list of query and hits gi in one file (file1) . i have another file in which complete name of hits is there(file2), now i want to replace Hits gi from file1 to file2 that have the complete Hit name. i want that gi must be replace with the…
Sidra Rafi
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How can I upload multiple sequences to BLAST using Biopython?

I am trying to run BLASTN searches of multiple sequences from a single FASTA file. I can easily query a single sequence from a file but am struggling to query all the sequences in one file. As these are relatively short reads, I would rather not…
user3076305
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Processing files line-by-line

I am processing a large BLAST file together with a large FASTA file, and I need to load several lines of FASTA for one block of BLAST (let's say it is one line). I would expect that in the second loop (line) of BLAST, it will continue on the next…
Kamil S Jaron
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Is there any way to get (a lot of) values from a file to filter a big xml using xmlstarlet?

everyone. I'm trying to filter a big xml file (from a BLAST) to keep only some nodes defined by a list of values that I define from a file. Here is a simplified example (the real Blast.xml have more than 80000…
anpefi
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Local BLAST Swissprot Database error

I am trying to run the standalone ncbi-blast-2.2.28+ on my machine (Mac) but get this error message when running blastp with SwissProt database: BLAST Database error: Could not find volume or alias file (nr.00) referenced in alias file…
lqdo2000
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What could be the max width of an HTML email blast?

I made html email blasts that are supposed to be supported in almost every email (gmail, yahoo, aol, outlook, etc.). I always set the width to 650px for the html email blast, but now I set it to 990px. I need to know whether this will be a problem…
Lucas Santos
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why I get different output running the same program in two different machine with same specification

I have a python program which uses bio-python and blast and it accepts the command line. I run this program on Centos 5.3 final. The problem is that I have this on two different machine with exactly as I know same application and same operating…
Ali_IT
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for loop is not working within my script

I made a script in bash that run blastx. #!/bin/sh -l # $Id: Barrine.sh federicogaiti $ echo "Right now it is:" date echo "" function usage() { echo "Barrine.sh script by Federico Gaiti, March 2013." echo "" echo "Run Blastx" echo "" echo "Usage:…
user1819854
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Port desktop to web application (bioinformatic)

I want to port a few bioinformatic programs which I wrote for Windows OS to web applications. I'm using a few bioinformatic packages like BLAST, Bowtie or Primer3. These external tools usually take a file which the user provides, processes it and…
honeymoon
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make Blast search take longer time

i am referring to this link : http://www.ncbi.nlm.nih.gov/books/NBK52637/ , to try blast search on the single machine. I had dl the blast app and refseq_rna blast database from the NCBI website. The blast search take only few seconds to get the…
bridgecarter
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Biopython cannot find file

I am trying to run a qblast from the Python prompt and after importing all the libraries I need, Python cannot find my file: >>> record = SeqIO.read(open("sinchimeras_1.fasta"), format="fasta") Traceback (most recent call last): File "", line…
Ma_fermar
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Syntax error running BLAST online with Biopython

I am trying to build a script to compare my fasta files from pyrosequencing with the nucleotide GenBank database following the Biopython Tutorial and Cookbook (Chapter 7). While the process is running, the prompt shows the following…
Ma_fermar
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