Question: Can we use JELLYFISH for amino acid seqeunces?
0
gravatar for marksingh1982
4 days 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 • 78 views
ADD COMMENTlink modified 4 days ago by Sej Modha2.5k • written 4 days 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 4 days ago by Ram13k
1
gravatar for Sej Modha
4 days ago by
Sej Modha2.5k
Glasgow, UK
Sej Modha2.5k 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 4 days ago by Sej Modha2.5k

Thank you for your quick reply!

ADD REPLYlink written 4 days ago by marksingh19820
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