Failed Blast2GO blastX and annotation

[Erick Awuoche]

I did a blastX using Blast2GO tool against non redundant NCBI protein database for 13569 contigs of the sequences of Trypanosoma congolense fasta transcripts sequences I downloaded from the TrytripDB. I only got results for 1356 sequences. I used the cloud for the Blast2GO pro. I want to perform functional and enrichment analysis of my transcriptome data. I don't know why this has happened. Could someone help me how to go about it.
Thanks,
Erick

[sgoetz]

Hi, some questions which might help.

How many sequences got significant (good) blast results? There are several charts in Blast2GO which might help: the amount of hits you got for each seq, the e-value distribution and the similarity distribution.
Second thing is the mapping. How many of your blast hit got linked with gene ontology terms (i.e. how many sequences turned green)? Of course, you can not annotated more sequences than that.
Once we know these things we might find out what your issue is.

In general, if you get low annotation coverage you could try to run InterPro Scan which might give you additional functional information based on domains. The order is: Blast, Map, Annotate, InterProScan and finally Merge InterProScan based annotations to existing ones.

I guess you used default parameters throughout the analysis - because obviously a change of these can also affect the annotation performance in terms of quantity and quality.

[yzzhang]

which software and parameters you used for gene prediction? you said "for 13569 contigs of the sequences of", did you mean you blasted the contigs directly against nr database?