Can we use JELLYFISH for amino acid seqeunces?
1
1
Entering edit mode
3.8 years ago

I have a very large file of 1000's of amino acid sequences. I would like to identify ALL overlapping k-mers.

I was hoping to use JELLYFISH, but it only seems to work with nucleic acid sequences. Is there any way to use the tool to read and parse the fasta file of amino acids?

jellyfish genome sequencing • 1.1k views
ADD COMMENT
0
Entering edit mode

This is a question; you're not posting about a tool. I've made the required change now, please be more careful in the future.

ADD REPLY
2
Entering edit mode
3.8 years ago
Sej Modha 5.0k

Jellyfish cannot deal with the protein sequences. You can use skbio iter_kmers() for this. BioPython solution:

from Bio import SeqIO
from skbio import Sequence

myfile=SeqIO.parse('test.fa','fasta')
for record in myfile:
    sequence=Sequence(str(record.seq))
    for kmer in sequence.iter_kmers(4, overlap=True):
        print(str(kmer))
ADD COMMENT
0
Entering edit mode

Thank you for your quick reply!

ADD REPLY

Login before adding your answer.

Traffic: 2324 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6