gene ontology

[ssing]

Hi all,

I am trying to do some pretty naive gene ontology profiling of my RNAseq data. These data are from a de novo assembly of a lizard genome. In the past, I had used Blast2Go, but I have found it somewhat clunky to navigate.

What other options are there? I have tried downloading the GO term databases from geneontology.org, but I am not sure where to go from there. So, now, I have a list of my contigs, the gene to which they match, and a set of GO terms to which the genes match. Would it be as simple as figuring out what those GO terms mean and counting up the different categories?

Best,
sonal

[SES]

Hi all,

I am trying to do some pretty naive gene ontology profiling of my RNAseq data. These data are from a de novo assembly of a lizard genome. In the past, I had used Blast2Go, but I have found it somewhat clunky to navigate.

What other options are there? I have tried downloading the GO term databases from geneontology.org, but I am not sure where to go from there. So, now, I have a list of my contigs, the gene to which they match, and a set of GO terms to which the genes match. Would it be as simple as figuring out what those GO terms mean and counting up the different categories?

Best,
sonal

I agree about Blast2GO. The BLAST output is their own XML format and other analyses are difficult to write out in a text form (it has been years since I tried it though).

You can do this by reading through a mapping file that contains a gene/protein name => GO term mapping. Then, you just need to find the gene/protein name match for you contig and write the GO term.