gene annotation for a large number of genes

[Tom2013]

Hello,

I have around 60 000 genes from RNA-seq data. I have blasted each sequence to the nr database and obtained a xml file. Does anybody know what softwares can be used for down stream GO term mapping and annotation by using the xml file as input? Thanks.

[colindaven]

Which species ? Pedant is good

http://pedant.gsf.de/

Some use Blast2go but I always had network problems with it several years ago.

[sgoetz]

Blast2GO will accept your NCBI Blast+ generated XML file for import. You can provide one file of multiple XMLs, multiple files as well as a folder. Blast2GO supports the latest version XML2 as well as the previous XML format. Mapping the HIT ids against the GO and further functional annotation should be straightforward.

[Tom2013]

Thanks for your replies. I have done annotation.

[GenoMax]

Did you use one of the options mentioned above or something different? It would be useful to include that information for benefit of others who find this thread via a search in future.

[Tom2013]

I used blast2go for mapping and annotation. The B2G pro is very fast for GO term mapping and it is very easy to use.