how to download sequences of gene product associated with certain GO term

Question

[sckinta]

Hi

In Gene Ontology, we find a certain GO term of interest. When looking into the GO term, I found more 10000 gene product associations. (example : http://amigo1.geneontology.org/cgi-bin/amigo/term_details?term=GO:0016032#lineage) How can I get those 10000 gene product sequences? I tried to use web directly but request size cannot be bigger than 1000 genes. Any R package or Perl package can solve this problem?

Answer 1

[Denise CS]

Have you seen biomaRt?

Answer 2

[EagleEye]

Try GeneSCF perl based (works on LINUX and windows 10 bash1607). GeneSCF can be used for

• gene enrichment analysdis with your gene list
• Download complete terms and genes as plain text format (TAB separated table)