Question: Finding gene names of a fasta file contains gene sequences
0
gravatar for dark_rider_2010
2.3 years ago by
dark_rider_201010 wrote:

I have a fasta file contains sequence of 800 genes. The genes belong to different livings and I need to get list of gene names as output. I tried blast site, but the results of blast is a very long list for every gene.

blast gene • 1.2k views
ADD COMMENTlink modified 2.2 years ago by Biostar ♦♦ 20 • written 2.3 years ago by dark_rider_201010
1

Your question is not clear. You want gene names from fasta file ? Or you want to map description of each gene which is in your fasta file ? What type of ID you have ?Kindly elaborate and explain more clearly

~C.

ADD REPLYlink written 2.3 years ago by Chirag Parsania1.6k

oh I'm sorry. My fasta file contains a sub-sequence from genome of a living (which I don't know what it is). I don't have any ID of the gene except its sequence. I need to know an ID of the gene (gene symbol, entrez ID, etc). So I want to know the gene names of sequences in fasta file.

ADD REPLYlink written 2.3 years ago by dark_rider_201010
1

OK. Blast is the way to go. Once you get the blast results get first hit for each query. Default blast result gives you first hit as most confidant hit.

-C.

ADD REPLYlink written 2.3 years ago by Chirag Parsania1.6k

I'm not sure, but I think Kraken is what you need.

ADD REPLYlink written 2.3 years ago by WouterDeCoster41k

Wow, I didn't know Kraken at all, is there any online version of it?

ADD REPLYlink written 2.3 years ago by dark_rider_201010

I don't think there is. You need to run it locally.

ADD REPLYlink written 2.3 years ago by genomax73k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1904 users visited in the last hour