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Counting genes based on GO terms

Lets say I have a list of gene IDs. I want to assign them GO terms and then make a chart that shows how many times a GO term showed up on the list of genes. Like a bar graph with GO terms on one axis. However, I cannot use blast2go because I only have a list of genes and no sequences, and blast2go basic requires you to input sequences to work. I do not want to buy blast2go pro either. I've had limited success with PANTHER, however I want to be able to adjust the "levels" of GO terms that I can use. So by that I mean I might want to have the GO terms specific enough where "mitotic nuclear division" may be a GO term as opposed to "cell cycle".

Can anyone suggest a good program that can do this? Thanks!

Edit: I am analyzing a non-model organism. Most of these web-based programs that have pre-formatted gene IDs for a specific species will not work on my dataset.

gene-ontology rna-seq annotation
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updated by Ram Ram • written by kevluv93 kevluv93

REVIGO can summarize all of gene IDs belong to a GO term, and in the result page of AGrigo analysis with affy IDs as entry, you can see how many IDs mapped to a GO id...you know i like to help too much even my answer is irrelevant...

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written by zizigolu zizigolu

3 answers

Does this webtool get you at least part way? http://go.princeton.edu/cgi-bin/GOTermMapper They also have a GO Finder tool that might be of interest.
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written by Steven Lakin Steven Lakin

Have you seen GOSemSim package?

I think you can use its procedures to get what you want.

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written by Na Sed Na Sed

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