Searching for a site or program that can do functional annotation not being blast2go or david

Question

[ary.dantas161189]

I have a gene list of 13 thousand IDs from genebank and David is not recognizing my list. For some reason, when I try to upload it to do the funcional annotation it does not recognize the acecssion numbers.

Do you guys know any other site I can use to do this annotation?

My lab also does not have the Blast2go license, and the free version is too slow!

Thanks!

[GenoMax]

Post a few examples when posting a question such as this.

[ary.dantas161189]

Shall I post examples of my accession numbers? Or what kind of examples? I am new to the website, getting used to it yet

[GenoMax]

Yes. Some accession numbers that you are not able to map in DAVID. Also indicate the organism they are from.

[ary.dantas161189]

I am working with a brown spider, (Loxosceles genus), here are some accesions devid ins not recognizing, all of them are in that format and he can't recognize any of them

XP_015923007.1 XP_015923005.1 XP_015923001.1 XP_015923000.1 XP_015922998.1 XP_015922997.1 XP_015922996.1 XP_015922994.1 XP_015922990.1 XP_015922988.1 XP_015922982.1 XP_015922971.1 XP_015922964.1 XP_015922962.1 XP_015922960.1 XP_015922958.1 XP_015922948.1 XP_015922942.1 XP_015922941.1 XP_015922930.1 XP_015922924.1 XP_015922923.1 XP_015922921.1 XP_015922911.1 XP_015922910.1 XP_015922909.1 XP_015922907.1

[GenoMax]

Please use ADD REPLY/ADD COMMENT when responding to existing posts to keep these threads logically organized.

One of the reasons the ID's are not mapping is those are all "predicted" (XP*) accession numbers.

[ary.dantas161189]

sorry about the reply coment!

I did not know the XP part, I took these accession numbers straight from the blastx output. Is there another kind of ID given by Blastx that cold be used?

[GenoMax]

Any ID's that don't start with X* should (in theory, e.g. things that start with N* would be from RefSeq) fare better in terms of getting them mapped. Did you select just the top "hits" from your blast? What blast database was your search done against?

[ary.dantas161189]

Sorry for the delay, since I am new I was blocked after 5 posts, just got back to the pc now.

We prepared a list using only the top hits from the BLAST results, and we ran the Blastx agains the nr-database that was downloaded in our university's server.

Answer 1

[Israel Barrantes]

See here: A: From FASTA file to GO-annotation

Answer 2

[Marge]

I used gProfiler in the past and I quite like it (comprehensive output, flexible, fast, etc). I am not sure how well it could perform on a 13k input though (in general the set seems a bit on the large side to get informative functional enrichment).

[ary.dantas161189]

I am going to check it! The problem is I am working with a spider, so usually when I have to select an organism it is hard to come by spiders on the list

[WouterDeCoster]

Please try to be as informative as possible in your question and mention the organism you are working on!

[ary.dantas161189]

Sorry for the delay, since I am new I was blocked after 5 posts.

I am working with a brown spider venom gland (Loxosceles genus), popular known in the US as brown recluse spiders.