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We now have a collection of transcripts at hand. We would like to investigate some particular ones, which are ion/water channel related. How to perform this? Could anybody point out how to find the annotated genes those are ion/water channel related? If there are some places particularly for fish, that would be perfect. Thanks.

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In case you don't know it, this should be of help: geneontology.org –  nico May 17 '12 at 7:05
    
i'm afraid a literature crawl is the only reliable way to get domain knowledge like this. –  shigeta May 17 '12 at 14:38

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I think your best bet is to blast your transcripts against the TCDB which has all ion channel templates you can get in the literature. Second best would be to blast against a general protein database like UniProt.

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