[hugh_hang]

I got the same problem. When i tried to import the xml file that was blatsted against Arabidopsis TAIR10 cDNA reference, the mapping and annotation steps failed in blast2go software. So i guess it is something to do with the format of xml file generated using "nr" database and "TAIR10" database.
Does anybody know a way to modify this xml file so that i can import to blast2go?

Thanks
Upendra

I've tried changing format but it doesn't work. I guess we should use TAIR10_pep... for BLAST DBs which is protein files.

[upendra_35]

I've tried changing format but it doesn't work. I guess we should use TAIR10_pep... for BLAST DBs which is protein files.

Sorry my bad.....i have used pep file and not cDNA file.

[kmcarr]

I've tried changing format but it doesn't work. I guess we should use TAIR10_pep... for BLAST DBs which is protein files.

Blast2GO is very particular about the format of the sequence ID used in FASTA files when you are creating custom BLAST databases. See this webpage for details about formatting your own BLAST DB for use with Blast2GO.

A second thing to consider is do the IDs in you custom BLAST DB ('myid' in the example on the webpage) match IDs in the Blast2GO database. If the IDs don't match, Blast2GO won't be able to map them. Even if you reformatted the TAIR FASTA like the example in the tutorial and put the AT number in the proper position I'm not sure that TAIR AT numbers are in the Blast2GO database.

A workaround is to use this file from the TAIR site: At_GB_refseq_prot.gz. It is the same protein set but uses the NCBI RefSeq IDs and GI numbers for the IDs. For example:

>gi|240256448|ref|NP_200529.4| PSD2 (phosphatidylserine decarboxylase 2); phosphatidylserine decarboxylase [Arabidopsis thaliana]

Format this file according to the tutorial. You are sacrificing the AT numbers but it's pretty much a guarantee that the NCBI GIs are in the Blast2GO database.

[upendra_35]

Blast2GO is very particular about the format of the sequence ID used in FASTA files when you are creating custom BLAST databases. See this webpage for details about formatting your own BLAST DB for use with Blast2GO.

A second thing to consider is do the IDs in you custom BLAST DB ('myid' in the example on the webpage) match IDs in the Blast2GO database. If the IDs don't match, Blast2GO won't be able to map them. Even if you reformatted the TAIR FASTA like the example in the tutorial and put the AT number in the proper position I'm not sure that TAIR AT numbers are in the Blast2GO database.

A workaround is to use this file from the TAIR site: At_GB_refseq_prot.gz. It is the same protein set but uses the NCBI RefSeq IDs and GI numbers for the IDs. For example:

>gi|240256448|ref|NP_200529.4| PSD2 (phosphatidylserine decarboxylase 2); phosphatidylserine decarboxylase [Arabidopsis thaliana]

Format this file according to the tutorial. You are sacrificing the AT numbers but it's pretty much a guarantee that the NCBI GIs are in the Blast2GO database.

Thank you very much kmcarr, very useful tips. Can't wait to start my Blast2Go annotation now. Thanks again.