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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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Biopython local BLAST database error

I am trying to run blastx locally with the "nr" database using Biopython's NcbiblastxCommandline tool but I always get the following error regarding the protein database search path: >>> from Bio.Blast.Applications import NcbiblastxCommandline >>>…
priyasshah
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Can I use BLAST to compare 2 non-biological strings?

I know what BLAST (The Basic Local Alignment Search Tool) was designed for. But I am interested in using such advanced text comparison and its final effects.
rzur2004
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BLAST Database allocation error

I asked this question on the bioinformatics version of stackexchange, but since I think it is a computer problem I thought I should try my luck here. When running local BLAST (v2.2.24+) on a big database (all human proteins) I get the following…
Niek de Klein
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wsimport import fails with NCBI/Blast

I'm trying to generate the files handling the SOAP services documented here: http://www.ncbi.nlm.nih.gov/books/NBK55699/ But wsimport fails: $ wsimport -d generated "http://www.ncbi.nlm.nih.gov/blast/netblast/blastws.cgi?WSDL" parsing…
Pierre
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Fastest way to perform BLAST search using a multi-FASTA file against a remote database

I have a multi-FASTA file having ~125 protein sequences. I need to perform a BLASTP seach against remote nr database. I tried using NcbiblastpCommandline, but the issue is that it only accepts files as input. Since my file has a huge number of…
accibio
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Why is Python's shutil.which() not working?

I'm trying to see if shutil.which() works for finding the blastn command from NCBI's BLAST. Running which blastn on my terminal results in /usr/local/bin/blastn. However, if I do shutil.which("blastn"), it simply returns None. Searching for Python…
blueblast
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Resources to learn how to manage tabular data (from BLAST+6 format ) using Bash and/or Biopython

I am running BLAST and would like to manipulate the output from using BLAST+6 format. For example, I would like to take the E-value, query coverage, and identity for each hit and then plug them into an equation that weighs all three into a single…
Bacteremia
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NCBI BLAST, nr database

I am running the command for BLAST : blastp -query /Users/shalini/Desktop/shalini/project/unmodelled_fasta/AAA18895.fasta -outfmt "7 sacc qcovs pident ppos evalue" -db=/Users/shalini/Downloads/nr…
shalini
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What is the time complexity of the given BLAST?

This is the BLAST(Basic Local Alignment Search Tool) graph. How can I calculate its time complexity?
LiaNalani
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Different Blast tools

I am currently looking for commercial vs. non-commercial blast tools. I've used several times the NCBI blast for my local blast searches but now I am looking for interesting alternatives. During my search I found some interesting results such as…
Beeth
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Finding the best reciprocal hit in a single BLAST file using python

I have a BLAST outfmt 6 output file in standard format, I want to find a way to loop through the file, select each hit, find its reciprocal hit and decipher which is the best hit to store. For example: d = {} for line in input_file: term =…
Gloom
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Run a shell script in R with multithreading

I want to run a shell script (BLAST+ in NCBI) in R with command system(), but it seems to use only one thread even if I set multiple threads in the shell script. What should I do to use multiple threads in this case? The code is system("blastp…
S.Wang
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Execute an external BLAST program in PHP

I want to execute a blastx search application in PHP instead of Linux console text terminal. The actual command line arguments would be (see definition of refer): ./blastx -query $input -db ${Sbjct}_db -evalue 0.0001 -outfmt 6 -out…
Penny Liu
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Error when using NCBIWWW from biopython

I am trying to blast nucleotide sequence using NCBIWWW from Bio.Blast import NCBIWWW my_query = "TGCGTGCCGTGCAATGTGCGT" result_handle = NCBIWWW.qblast("blastn", "nt", my_query) blast_result = open("my_blast.xml", "w")…
reut
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Fast Sequence Alignment on Unicode Strings

I want to run something like the BLAST algorithm to query a large database of unicode strings. Most of the alignment software like BLAST expects nucleotide or protein strings as input. But my input could potentially contain any unicode character. …
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