Obtaining alignment from psiblast
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6.8 years ago
nilus1432 ▴ 30

Hi everyone,

I am using stand alone version of Psi-blast. 

I want to get just the query sequence followed by matched-hit sequences (both aligned) in fasta format.

How to do it in Biopython or stand alone blast.

1. Some posts suggest Mview: for some reason this solution i am not using

2. I can get qseq and sseq using -outfmt 6 option but not full sequences in aligned format.

3. Similar to 2 i am able to get with biopython but again not full aligned sequences as i need

Thanks for help

-nil

alignment sequence blast snp • 3.1k views
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6.8 years ago
a.polo88 ▴ 110

perhaps :

 

in  Ubuntu/Debian   NCBI   tools  available  by  installing  the package blast2 (or   the       newest ncbi-blast+)
(sudo) apt-get install blast2 or (sudo) apt-get install ncbi-blast+ another useful tool is formatdb

 

For blast2 users!
formatdb –i <db_fasta_file>
For blast+ users (on Linux or Windows)
makeblastdb –in <db_fasta_file> -dbtype prot

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6.8 years ago
nilus1432 ▴ 30

I already have local blast, I want formatted output, any idea??

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6.8 years ago
a.polo88 ▴ 110

an example perhaps  of formatted output can be :

psiblast -query CCL25_HUMAN.fa -db UniprotKBSP.fa -evalue 0.0001 -num_iterations 3 -out_ascii_pssm CCL25_HUMAN.pssm –out CCL25_HUMAN.alns.blast

where :

Input       sequence:        CCL25_HUMAN.fa!
 Search       database:       UniprotKB/SwissProt       ( UniprotKBSP.fa)       
E-­‐value       threshold:       0.0001       
Output       file       for       pairwise       alignments:        CCL25_HUMAN.alns.blast
Output       file       for       PSSM/Profile       matrices:        CCL25_HUMAN.pssm
Three       itera<ons       (-­‐j       3)      

if you ask for this, otherwhise you can see other parameters simple with the help() command if you use one of these programs.

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6.8 years ago
Siva ★ 1.8k

I don't think there is any option in PSI-BLAST to output the multiple alignment.

I remember buildali.pl of HHsuite used to have an option to extract the multiple alignment in FASTA format from PSI-BLAST result. It now uses CS-BLAST instead of PSI-BLAST. However, I found a version of buildali.pl (probably an older version) whose description says that it extracts multiple alignment from PSI-BLAST result.

There is also another tool called Blammer from HHsuite that converts BLAST/PSI-BLAST result in to multiple alignments.

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Yes, this is what i am looking for. I tried buildali.pl on the psiblast output (version 2.2.30) which was run using "psiblast -query fasta -db database -num_iterations=3 -out out.align".

However, the buildali.pl terminates with a error 

"Error in alignhits.pl: blast output file out.align truncated:"

Any suggestions??

Thanks

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