Question: blastn many pairs of DNA sequences
0
gravatar for cddiligent
3 months ago by
cddiligent0
cddiligent0 wrote:

Hello all

I have 2 fasta files containing the same number of sequences. I'd like to blast them pairly (seq1 in file 1 to seq1 in file 2, seq2 in file 1 to seq2 in file 2 ......) and get the highest match for each pair. For example:

file1.fa

>a1
ATCGATAC

>b1
TAAATGTCGA
...

file2.fa
>a2
TGACGCTG

>b2
AGCGATGA
...

I want to blast a1 to a2 and b1 to b2 ......

Is there a good way to perform this?

Thank you a lot.

blastn • 183 views
ADD COMMENTlink modified 3 months ago by Prasad1.6k • written 3 months ago by cddiligent0

I want to blast a1 to a2 and b1 to b2 ......

Your best bet is to split the sequences into individual files (How to split a multi fasta file into individual chromosomes ) and then do the blasts you need. Otherwise you could simply do an all against all blast search and pick out results you need.

ADD REPLYlink written 3 months ago by GenoMax96k

Thank you. I thought about separating them, but there are >1000sequences in each file. I will try blasting all against all, if it won't take too long to finish.

ADD REPLYlink written 3 months ago by cddiligent0

If you are not performing blind BLAST search (ex: against entire nr/nt), why not map using a read mapper (ex: bowtie) against reference sequences by taking these 2 files are paired data. This way you can also get an advantage of filtering out the mapping based on inner distance between each pair.

ADD REPLYlink modified 3 months ago • written 3 months ago by Prasad1.6k
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