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Old 10-13-2015, 07:47 AM   #1
Tom2013
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Default gene annotation for a large number of genes

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.

Last edited by Tom2013; 10-13-2015 at 08:14 AM.
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Old 10-13-2015, 07:57 AM   #2
colindaven
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Which species ? Pedant is good
http://pedant.gsf.de/

Some use Blast2go but I always had network problems with it several years ago.
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Old 10-21-2015, 02:56 AM   #3
sgoetz
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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.
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Old 10-21-2015, 06:54 AM   #4
Tom2013
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Thanks for your replies. I have done annotation.
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Old 10-21-2015, 07:26 AM   #5
GenoMax
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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.
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Old 10-21-2015, 07:33 AM   #6
Tom2013
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I used blast2go for mapping and annotation. The B2G pro is very fast for GO term mapping and it is very easy to use.
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