Protein sequence comparison and Protein evolution.pdf

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1、ProteinsequencecomparisonandProteinevolutionTutorial-ISMB2000WilliamR.PearsonDepartmentofBiochemistryandMolecularGenetics,JordanHall,Box800733UniversityofVirginia,Charlottesville,VA22908,USAOctober,2001Contents1Introduction21.1Evolutionarytimescales.....................

2、.............41.2Similarity,AncestryandStructure.............................61.3ModesofEvolution.....................................81.3.1Conventionaldivergencefromacommonancestor................81.3.2Sequencesimilarityandhomology,theH+ATPase................101.3.3Prot

3、einfamiliesdivergeatdifferentrates.....................161.3.4Mosaicproteins...................................181.4IntronsEarly/Late......................................181.5DNAvsProteincomparison................................192Alignmentmethods222.1Algorithms.......

4、..................................222.2DynamicProgrammingAlgorithms............................252.3HeuristicAlgorithms....................................27FAX:(804)924-5069;email:wrp@virginia.EDU12.3.1BLAST.......................................292.3.2FASTA...........

5、............................293Thestatisticsofsequencesimilarityscores303.1Sequencealignmentswithoutgaps.............................313.2Scoringmatrices......................................313.3Empiricalstatisticsforalignmentswithgaps........................353.4Statis

6、ticalsignificancebyrandomshuffling........................364Identifyingdistantlyrelatedproteinsequences364.1Serineproteases.......................................374.2GlutathioneS-transferases.................................424.3G-protein-coupledreceptors................

7、................435Repeatedstructuresinproteins466Summary48References507SuggestedReading527.1GeneralProteinevolution..................................527.1.1IntronsEarly/Late.................................527.2Alignmentmethods.....................................527.2.

8、1Algorithms.....................................527.2.2Scoringmethods..................................