Question: Running Blast For A List Of Pairs
gravatar for Freddie
6.4 years ago by
Freddie0 wrote:


I would like to ask if it is possible that I run BLAST with a list of pairs of query and reference sequence IDs?

I tried bl2seq but unfortunately it does not produce the alignment of the whole length. So, for example, if a pair of sequences can produce 4 alignments, then bl2seq will output 4 results for each alignment, each with its own percentID value, while blastall extends and joins all the alignments together, and so it produces only one value of percentID of the whole. I would like to be able to run like this blastall but for all pairs that I have selected whose ID I have put in the list. Is this possible?

Thanks heaps.

blast blast+ • 3.0k views
ADD COMMENTlink modified 6.4 years ago by Hamish3.1k • written 6.4 years ago by Freddie0

by the way, this is for protein sequence.

ADD REPLYlink written 6.4 years ago by Freddie0
gravatar for Joseph Hughes
6.4 years ago by
Joseph Hughes2.7k
Scotland, UK
Joseph Hughes2.7k wrote:

You could do a blastall of the IDs you are interested in against database of the reference you want to use. Create a fasta file with you sequences to compare to, e.g. reference.fa. Format the database:

makeblastdb -in reference.fa

Then blast your set of interest against this database

blastp –db input.fa –query input.fa –out results.out

The output will provide you with the percent identity for the length of your query.

ADD COMMENTlink written 6.4 years ago by Joseph Hughes2.7k
gravatar for Hamish
6.4 years ago by
Hamish3.1k wrote:

In NCBI BLAST+ the pairwise alignment capability that was provided in 'bl2seq' has been merged into the main programs (e.g. blastp, blastn, blastx, etc.). For details of how to use the NCBI BLAST+ (and legacy NCBI BLAST) programs to perform pairwise alignments see:

And many of the other BLAST related questions on Biostar: blast

Depending on your requirements the pairwise local alignment provided by NCBI BLAST and NCBI BLAST+ might not be the most appropriate method. So you may want to look at the following:

For more options see the List of sequence alignment software page in Wikipedia.

ADD COMMENTlink written 6.4 years ago by Hamish3.1k
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