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Where can I find an online toolkit that provides functional similarity scores (in the form of a matrix) between two functional gene sets in the context of gene ontology?

I have tried the following:

  1. Batch tool for GSFS: PROBLEM: It says that my input yeast genes are not human genes (which probably means that the tool will work only with Human genes).

  2. http://bioinformatics.clemson.edu/G-SESAME/Program/geneCompareTwo1.php : PROBLEM: provides score for every gene pair input. I have ~3600 genes. Impossible to do it for eveyr pair.

  3. DAVID batch viewer gives a 1xN matrix (functional similarity score of one gene to a set of N genes, when I want all possible pairs of similarities which will give an NxN matrix)

  4. GO funsimmat- I am unable to get this to work, so I'm not sure if it will give me the desied results.

  5. GO FastSemSim- same as 4.

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I think that you could try a similar approach to GSFS:

  • use transduction in proteins (if you don't know star code, then you must use 3 strings for each gene)

  • use a basic tool (a stand alone like UNIPROT tools) to identify the proteic domain type (chain alpha, ..)

  • divide the genes by proteic domain type (pdt): which contains which pdt and the pdt order frequencies

Now, you could use DAVID or similar (try wconsensus: it's old, basic but very custom) to compare similar sequence and obtain your scores.

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