Stack Overflow
Stack Overflow

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

214 questions
0
votes
1 answer

blast given GI NCBI nucleotide database

I have local database driven website which contains a few sequences which are uniquely identified via their GI number. Is it possible to link to the 'NCBI blast site' directly given the GI. For example the sequence for GI 903049 has this…
cs0815
  • 13,862
  • 32
  • 107
  • 253
0
votes
1 answer

Can you use blastn to check for exact matches?

I need to know on which subjects a query has been matched and where, and this match has to be 100%. Is there a way to do this using blastall? Thanks.
gravitas
  • 703
  • 4
  • 16
-1
votes
1 answer

why is makeblastdb not working with syntax error

import sys sys.path.append('/home/minhlam/ncbi-blast-2.10.1+/bin/db') makeblastdb -in human.fa -db mouse.fa -out mousedb -outfmt 5 The error is: File "parseBlast.py", line 5 makeblastdb -in human.fa -db mouse.fa -out mousedb -outfmt 5 …
minjah
  • 7
  • 2
-1
votes
1 answer

Running BLAST in Python with Biopython for SARS Virus. My output is simply not showing up! Someone check my code?

Here is my code: from Bio.Blast import NCBIWWW result = NCBIWWW.qblast("blastn","nt",r"C:\Users\video\Documents\sars.fasta") save_file = open("blast4.xml", "w") save_file.write(result.read()) save_file.close() result.close() result =…
Johnn-1231
  • 15
  • 2
-1
votes
1 answer

How can i loop through all my .fasta files?

I wrote a code to go through all my .fasta files in my directory but it is not working. I want it to match with my -db Viral.fna and output (fasta file name).txt and -outfmt 6 I tried 2 different codes for f in file1.fasta file2.fasta etc ... do…
David Wakim
  • 27
  • 8
-1
votes
1 answer

How to write csv file in R for following data?

I want to get the Get taxonomic hierarchy using Accession Numbers. The simplest way i found to do is library('taxize') for (year in c("AY744148.1","AY656167.1","AY656168.1")){print(paste( year))} classification(genbank2uid(id = year), db =…
Ali Zohaib
  • 99
  • 8
-1
votes
1 answer

Parsing a long JSON using GSON

I'm trying to parse a very long JSON like this. { "BlastOutput2": [ { "report": { "program": "blastn", "version": "BLASTN 2.6.0+", "reference": "Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer,…
Bruno Andrade
  • 243
  • 3
  • 7
  • 17
-1
votes
1 answer

I need help finishing this bioinformatics program

I need to create a program that can take some text file called a fasta file and transform it to give the sequence_name, Domain_names, Start of Domain, end Of Domain. So a fasta file is just a text file that looks like…
Mohamed Elbashir
  • 9
  • 1
-1
votes
1 answer

Loop to wait for result or timeout in r

I've written a very quick blast script in r to enable interfacing with the NCBI blast API. Sometimes however, the result url takes a while to load and my script throws an error until the url is ready. Is there an elegant way (i.e. a tryCatch option)…
biomiha
  • 1,050
  • 1
  • 10
  • 21
-1
votes
1 answer

Perl Program error

I wrote a PERL program which takes an excel sheet (coverted to a text file by changing the extension from .xls to .txt) and a sequence file for its input. The excel sheet contains the start point and the end point of an area in the sequence file…
The Last Word
  • 193
  • 5
  • 24
-1
votes
1 answer

Using Biopython to run a BLAT search through NCBI

I'd like to run several BLAT queries with different sequences and then perform a multiple sequence alignment on the results. How can I use Python to run these BLAT queries? I know that there is a way to use BLAST, but I am not sure about BLAT.
cs4
  • 11
  • 1
-1
votes
2 answers

associate dictionary to a .txt file

I have created a dictionary of contigs and their lengths in file1. I also have file2 which is blast output in tabular format, which contains contig alignments (but not all of them) and some additional information like where match starts and finishes…
user3224522
  • 853
  • 6
  • 16
-2
votes
1 answer

blast tab limited out extraction

I have blast result like this.. GCA_001188035.1_1 GCA_001188035.1_1 100.00 159 0 0 1 159 1 159 8e-113 324 GCA_001188035.1_1 GCF_000878595.1_1595 100.00 159 0 0 1 …
user3295716
  • 21
  • 5
-2
votes
2 answers

Completing a form on the internet using Python and downloading a result

I'm currently working on a python script and I am stuck. My script should go on a webpage, upload a file from the computer, fill a form, start an action (BLAST) and then wait since the action can be long. (sometimes one hour). After all this go on…
Axel Uran
  • 5
  • 2
-2
votes
1 answer

Find sequences that does not match to a target sequence

An interesting question by Rnaer from Biostar: I want to find unique dna/protein sequences of a given length (30nt, for example) that does not match to any region of the C.elegans genome. Is there any tool to do that?
hello_there_andy
  • 1,821
  • 2
  • 17
  • 48
1 2 3
…
14
15