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Protein Analysis (Beyond BLAST). Basic Protein Data (MW, pI) Generalized Features Multiple Sequence Alignments Fingerprints, Profiles, Domains Using Structure. Multiple Sequence Alignments Comparison of Methods. DIALIGN.
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Protein Analysis (Beyond BLAST) • Basic Protein Data (MW, pI) • Generalized Features • Multiple Sequence Alignments • Fingerprints, Profiles, Domains • Using Structure
Multiple Sequence AlignmentsComparison of Methods DIALIGN At 368 LY-------- ---------- --AEVAYHNF APPHVTKNSY FAAILGHNNNPY54 383 AY-------- ---------- --EKWFRTDP RWAKCDEDVF FSELLGHD--VHML 273 HHyqrvshts hgefsfrlpg hlCRIAFHEF RHNGESKAAF RSRVLGHSGGBB003 298 IY-------- ---------- --CKFSYLAF APKNMEMNYW ITKVLGHEPNN15 390 AY-------- ---------- --EMFFRVDP RWKNVDEDVF FMEILGHD--Ecto 304 SH-------- ---------- --RTFk---- --NNCSINIW LTKTLLHE-- At 398 DLETSLSYMT YTL------- ---------- ---------- ----------PY54 411 DPDTQLAYKQ FKL------- ---VNFNPKW TPNISDENPR LAALQELDNDVHML 323 DKSTQNHYEG FELdskveti gvvDMGQNEA DKSYNKQL-- LKHLEQYDATBB003 328 DITTAFHYNR YVL------- ---DNLDDKA DNSLLTLL-- NQRIYTYVRRN15 418 DENTQLHYKQ FKL------- ---ANFSRTW RPEVGDENTR LVALQKLDDEEcto 326 ALDTSIFYSR FRI------- ---DKCStnr gewaf----- ---------- ClustalW PY54 FRTDPRWAKCDEDVFFSELLGHD--DPDTQLAYKQFKLVNFNPKWTPNISDENPRLAALQ 456 N15 FRVDPRWKNVDEDVFFMEILGHD--DENTQLHYKQFKLANFSRTWRPEVGDENTRLVALQ 452 Ecto K------NNCSINIWLTKTLLHE--ALDTSIFYSRFRIDKCS------------------ 342 VHML R-----HNGESKAAFRSRVLGHSGGDKSTQNHYEGFELDSKVETIG-------------- 343 At AP-----PHVTKNSYFAAILGHNNNDLETSLSYMTYTLPEDR------------------ 414 BBB03 AP-----KNMEMNYWITKVLGHEPNDITTAFHYNRYVLDNLD------------------ 344
Multiple Sequence Alignments • Method of choice depends upon goal of alignment • FMI – Thompson et al., 1999. Nucleic Acids Research 27:2682-90. A comprehensive comparison of multiple sequence alignment programs.
Multiple Sequence Alignment Protein/Position within SequenceSequence YNZ5_YEAST/135-152 RLCYNCNETGHISKDCPKO65639/100-117 SGCYNCGELGHISKDCGIQ94821/1600-1617 KGCFNCGEEGHQSRECTKBYR3_SCHPO/17-34 PRCYNCGENGHQARECTKO44758/570-587 RGCHNCGEEGHISKECDKGLH1_CAEEL/262-279 RGCFNCGEQGHRSNECPNO96068/51-68 KGCFKCGEEGHMSRECPQHEXP_LEIMA/43-60 TTCFRCGEEGHMSRECPNO46363/5-22 VTCYKCGEAGHMSRECPKHEXP_LEIMA/196-213 RKCYKCGESGHMSRECPS
Pattern Searches Ultimate Goal Atwood, 2000, Int. J. Biochem. Cell Biol. 32:139-55
Pattern Searches 3 Levels Atwood, 2000, Int. J. Biochem. Cell Biol. 32:139-55
Pattern Searches Hidden Markov Model Atwood, 2000, Int. J. Biochem. Cell Biol. 32:139-55