Question: Gene Prediction Softwares
0
gravatar for me.sr1510
2.3 years ago by
me.sr15100
me.sr15100 wrote:

Hi everyone!!!

I have a list of 54000 gene-ids I want to annotate all the genes. Is there any other R package or command-line software that I can use?

Plz help!!!

gene • 768 views
ADD COMMENTlink modified 2.3 years ago by Macspider3.0k • written 2.3 years ago by me.sr15100
3

your question is very vague!

Can you elaborate on what exactly you want to achieve? since you already have a gene number I assume it's functional annotation you're looking for?

ADD REPLYlink written 2.3 years ago by lieven.sterck7.9k

Sorry for the vagueness. U are right, I want to annotate the genes. I m trying to use geneSCF for the same as it is command-line based but I have NM and NR ids becoz of which it is giving errors. So kindly guide further. Is there any other command-line based annotation tool or any R package for the same.

ADD REPLYlink written 2.3 years ago by me.sr15100

So these are Refseq ID. What do you want to do with the annotation and which species they belong to? geneSCG is clustering them based on functional relevance but these are too many ids, probably the entire transcriptome. Tell specifically the aim of the design and what you want to perform.

ADD REPLYlink written 2.3 years ago by ivivek_ngs4.9k
0
gravatar for Macspider
2.3 years ago by
Macspider3.0k
Vienna - BOKU
Macspider3.0k wrote:

What I used:

https://www.blast2go.com/

But simply searching in google scholar will give you tons of papers where people did this in different ways. You can also homebrew it yourself, building blast databases and blasting sequences against them.

ADD COMMENTlink written 2.3 years ago by Macspider3.0k
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