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Do you want to asses the identity or the number of overlapping genes? You should attempt be present your question with more specificity.
I am analysing proteomic data. Basically, I have data several gene IDs scored for wild type strains and for knockout strain. My question is, how can I assess effectively genes that are identical. Is there some Bioinformatic tool that I can use?
I am sorry for being unspecific rikki.frederiksen :), but it is true, my question was not clear :). I hope it is now :)
Are you working with a genome? Transcriptome? How were they processed? Is it an assembly? Usually assemblies reduce redundancy by removing identical contigs. Are you working with peptides or spectral counts? What tools are you currently using the examine the proteome?