download nr database protein accession number to GO term file

Question

[fanglujing]

Hi, is there anyone have downloaded GO annotation file which contains nr database protein accession number and its related GO term? each line of this file may contain both nr accession number and go term. I didn't find it. If you have downloaded this file, please give me the download url, many thanks

[Puli Chandramouli Reddy]

Can you tell the name of you model organism?

[fanglujing]

well, I just wanna download the database and import it to mysql, so I can use mysql to annotate my blastx result. In most situation, I work on non-model organism.

[Puli Chandramouli Reddy]

Ok..

1. One way is to map nr ids to uniprot and get associated GO ids (it may not work if your model organisms information is not there in UniProt).

2. Another way is to annotate you nr database by InterProScan or Blast2Go.

[fanglujing]

thanks, I have tried the InterProScan, but I can't bear its annotation speed, I don't know if this software support blast tabluar or xml format result as its input. In fact, I employ the idea of blast2go, store database in mysql is more quicker than just use the python or perl annotation. But, you know, the free version of blast2go is not friendly and it also spend too much time to GO annotation. I also tried the b2gpipe(local blast2go), and this version is not free anymore. so I want to build my own light 'blast2go'. Anyway, too many thanks.

[Puli Chandramouli Reddy]

I have used InterProScan and it was fast enough to get the annotation. And also used BlastP (instead of Blast2Go) against UniRef90 (UniProt database) and output was used to make GAF file (GO annotation). I have combined the results from InterProScan and BlastP on UniRef90 and worked very well in identifying Transcription factors and Sign ling pathway components.

[fanglujing]

I'll try that way, I really appreciate it.