Question: Finding gene names of a fasta file contains gene sequences
0
gravatar for dark_rider_2010
21 months 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 • 1.0k views
ADD COMMENTlink modified 20 months ago by Biostar ♦♦ 20 • written 21 months 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 21 months ago by Chirag Parsania1.4k

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 21 months 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 21 months ago by Chirag Parsania1.4k

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

ADD REPLYlink written 21 months ago by WouterDeCoster38k

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

ADD REPLYlink written 21 months ago by dark_rider_201010

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

ADD REPLYlink written 21 months ago by genomax65k
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