Question: Can we use JELLYFISH for amino acid seqeunces?
0
gravatar for marksingh1982
9 months ago by
Boston
marksingh19820 wrote:

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?

sequencing jellyfish genome • 287 views
ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 9 months ago by marksingh19820

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 REPLYlink written 9 months ago by RamRS19k
1
gravatar for Sej Modha
9 months ago by
Sej Modha3.8k
Glasgow, UK
Sej Modha3.8k wrote:

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 COMMENTlink written 9 months ago by Sej Modha3.8k

Thank you for your quick reply!

ADD REPLYlink written 9 months ago by marksingh19820
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