0 mapping hits for blast2go

Question

[4galaxy77]

Hi, I've blasted all of my differentially expressed genes using blast2go and got about 70 hits which reach the right e value threshold - but when I run the mapping function, it takes about 2 minutes and says that none of the sequences are actually mapped. Does anyone know why this might happen?

Thanks

[4galaxy77]

When you say blast program - what do you mean exactly. I used the NCBI blast using tblastx with a threshold of 1e-5. Also, where is the table button you mention?

Thanks,
S

Answer 1

[Prash]

Dear Morris

I am not sure if you used an inadequate blast program. Could you click "Table" and see instead?

Regards
Prash

Answer 2

[Chris Fields]

Have you had a look at the BLAST2GO FAQ? This seems similar to the question on that page: 'Some of my sequences have low blast e-values and mapping results but failed to get annotated. Why?'.

[4galaxy77]

I think that question refers to not getting annotation results, which is what occurs after the mapping. I am unable to map my hits in the first place.

[Chris Fields]

Are you loading in your own BLAST results or running it within BLAST2GO? The same FAQ mentions this issuing if loading in BLAST XML format.

The BLAST2GO Google group also has a few posts regarding this problem and possible reasons for this.

Alternatively, maybe this BioStar answer?

[4galaxy77]

Yeah thanks, that seems to have sorted my problem. I changed the blast program from tblastx -> blastx and it's giving me some mapping results now. cheers.