Tools for sequence data mining: HMMER (part 2)

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HMMER

Profile hidden Markov models for biological sequence analysis

http://hmmer.wustl.edu

RepeatAnalyzer - Computational Biology Service Unit (CBSU)

MODELLER - Computational Biology Service Unit (CBSU)

Linux for Biologists - CBSU @ Cornell University

HMMER Profile hidden Markov models for biological sequence analysis http://hmmer.wustl.edu

40ptsH 41ptsH 42rhaS 43rot TTTTGTGGCCTGCTTCAAACTT TTTTATGATTTGGTTCAATTCT AATTGTGAACATCATCACGTTC TTTTGTGATCTGTTTAAATGTT Alignment Model GTGTGATCAGAGTGATTGTGTCAGTGTGTAGCGCTCTGTT TCGTGTGTTTGTGTTCATTTATTGTGTTGT GGCTTCTCATT GCCCCTTTGGTTCTGTTCTTAAACCTTCATCTTCGCTTAGT AAAGTTAGATTCCACCGA TCCGTTTCTGTTA AAGAAAAAG TGATCAACAAACTTCAAGAAAATCTAAATGTGCAGTAATTT GAAATTTATGCTTATTGTGT Search for matches

Page 1: Searching for similar proteins in a
Page 5 and 6: HMM libraries: PFAM: http://pfam.wu
Page 7 and 8: Program 1: hmmpfam Search an HMM da
Page 9 and 10: Evaluating the significance of a hi
Page 11 and 12: Program 2, 3. hmmbuild & hmmsearch
Page 13 and 14: Automated Process: Training Sets:

Tools for sequence data mining: HMMER (part 2)

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