compare two list of nucleotide sequences

Dear all,

I have a list of nucleotide fasta sequences which has to be compared to another list of nucleotide sequences and output which two sequences are an exact match without any gaps or mismatches.

Eg.

List A

>query1
sequence
>query2
sequnce
>query3
sequence

List B

    >subject1
    sequence
    >sub2
    sequence
    >sub3
    sequence

Example output

query2 == sub3

I want to know, if the solution already exists, if not how shall I approach it

Thanks KK

blast bowtie mummer sequence

• 3,431 views • link

updated 7.8 years ago by Joe

• written 7.8 years ago by karthic

1 answer

You can do this easily with BioPython.

This is some code just off the top of my head so may not be 100% correct, but should get you started.

import sys
from Bio import SeqIO

GenesA = list(SeqIO.parse(sys.argv[1], ‘fasta’))
GenesB = list(SeqIO.parse(sys.argv[2], ‘fasta’))

matches = []
for i in GenesA:
    for j in GenesB:
        if i.seq == j.seq:
             matches.append(i)

for seq in matches:
    print seq.format('fasta')

This isn’t the fastest or most elegant way to do it, but it is safe because it doesn’t assume your lists are the same length or anything.

• 1 views • link

written 7.8 years ago by Joe

Hi jrj healey,

Thanks for the code, I will start with that and let you know.

Thanks KK

• 1 views • link

written 7.8 years ago by karthic

Hello jrj.healey ,

but this would print out all sequences from GenesA that have a match in GenesB, wouldn't it. If I understood OP correct, (s)he want's a table o ids which have the same sequence. So your code should look something like this:

import sys
from Bio import SeqIO

GenesA = list(SeqIO.parse(sys.argv[1], ‘fasta’))
GenesB = list(SeqIO.parse(sys.argv[2], ‘fasta’))

matches = []
for i in GenesA:
    for j in GenesB:
        if i.seq == j.seq:
             matches.appendi.id+" == "+j.id)

for m in matches:
    print(m)

(Also just off the top of my head)

fin swimmer

Edit: There seems to be a bug in biostars. It removes the open brace here matches.append(.

• 1 views • link

written 7.8 years ago by finswimmer

Right you are, I didn’t read that bit properly.

OP will have access to the whole SeqRecord object inside matches and can print it out however they wish (I originally had the printing lines commented out because I wasn’t sure what output was desired (e.g. to a file or to screen etc)).

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written 7.8 years ago by Joe

Hi fin swimmer

I have noticed that and added that open brace, thank you for the solution.

Thanks KK

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written 7.8 years ago by karthic

Dear Jrj Healey and fin swimmer,

Thank you for the solution and the code. It is working and the results are just as I expected.

Thank you very much KK

• 1 views • link

written 7.8 years ago by karthic

Ok great, you're welcome.

Be sure to accept the answer (the check mark on the left of the post) if this is resolved for you.

• 1 views • link

written 7.8 years ago by Joe