BIOL 4020 Lecture Notes - Lecture 4: Retinol Binding Protein, Lipocalin, Blosum
23 Nov 2017
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Finding modules/domains in a protein - use blast, or can do so experimentally: eg: kinase, src, had common sequences with other domains, so called it src 1, src 2 etc. Conserved domain database search: input sequences, result is the expect value, the confidence with which you can say it"s the same domain. Eg: 2^-11 expect value is a good confidence level - likely the same domain. Cdart web server - input sequences and shows other proteins with same domains. Searching databases for matches that are highly customized to your sequence: *uncovering distant sequence relationship, results in sequences that have some differences, which are used again to refine the search - more. Iterative: using something over again - uses the query sequence many times to refine the results variability and a wider range of results. Seeing all the possible relations to your query sequence. First iteration: normal blast- close sequences to your query.
