Dear Tom, Hi

Of course you have mentioned "without using commercial Blast2GO", but the annotation and GO assignment procedure can be done with Blast2GO basic (free) version.

If your blast is in xml format (-outfmt 5), you can import your transcript sequence first and then import blast result on the same project Blast2GO and then run the annotation and mapping and GO assignment and after that export the .annot result freely from Blast2GO.

Then you can manipulate this file and use it in WEGO.

Trinotate would be one of your another choices.

~ Best

When I call the mapping step on Blast2Go (v4) I get the following information displayed, under two titles; 'Mapping Configuration'-'Mapping the Blast Hits of each sequence with Gene Ontology Terms'.

Blast2GO performs different mapping steps to link all Blast Hits to the functional information stored in the Gene Ontology database. Therefore Blast2GO uses different public resources provided by the NCBI, PIR and GO to link the different protein IDs (names, symbols, GIs, Uniprots, etc.) to the information stored in Gene Ontology database

It could be difficult to find the exact steps they use but I am able to find same GO annotations Blast2GO finds for my few sample BLAST searches using UniProt REST queries alone:

• In Blast2GO, i right click my query sequence and select 'Show Blast Result' to find accession numbers for matched sequences

• I then query UniProt with these accession numbers and ask to return the entry names and GO annotations only, as in the following example queries

  http://www.uniprot.org/uniprot/?query=WP_048113166.1&columns=id,entry%20name,go&format=tab http://www.uniprot.org/uniprot/?query=WP_007692371.1&columns=id,entry%20name,go&format=tab