Bioinformatics Slides (PDF) - Genomics & Medicine - Stanford ...

Discovering Function from Protein SequencePSSMs or Weight MatricesPosition1 2 3 4 5 6 7 8 9 10 11 12Consensus Sequencesor Sequence MotifsZinc Finger (C2H2 type)C X{2,4} C X{12} H X{3,5} HA 2 1 3 13 10 12 67 4 13 9 1 2R 7 5 8 9 4 0 1 16 7 0 1 0N 0 8 0 1 0 0 0 2 1 1 10 0D 0 1 0 1 13 0 0 12 1 0 4 0C 0 0 1 0 0 0 0 0 0 2 2 1Q 1 1 21 8 10 0 0 7 6 0 0 2E 2 0 0 9 21 0 0 15 7 3 3 0G 9 7 1 4 0 0 8 0 0 0 46 0H 4 3 1 1 2 0 0 2 2 0 5 0I 10 0 11 1 2 10 0 4 9 3 0 16L 16 1 17 0 1 31 0 3 11 24 0 14K 3 4 5 10 11 1 1 13 10 0 5 2M 7 1 1 0 0 0 0 0 5 7 1 8F 4 0 3 0 0 4 0 0 0 10 0 0P 0 6 0 1 0 0 0 0 0 0 0 0S 1 17 0 8 3 1 3 0 2 2 2 0T 5 22 3 11 1 5 0 2 2 2 0 5W 2 0 0 0 0 0 0 0 0 1 0 1Y 1 0 4 2 0 1 0 0 2 4 0 1V 6 3 1 1 2 15 0 0 2 12 0 28QueryDatabaseSequences ofCommonStructure or FunctionSequence SimilarityProfles, PSI-BLASTHidden Markov ModelsD 2 D 3 D 4 D 5I 1 I 2 I 3 I 4 I 5AA1 AA2 AA3 AA4 AA5 AA610 20 30 40 50VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF------DLSHGS|:| :|: | |:|||| | |:||| |: : :|:| :| | |: |HLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGN10 20 30 40 50