Giri Narasimhan

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ProteinDatabases used by BLASTnr (everything), swissprot, pdb, alu, individualgenomesNucleotideMiscnr, dbest, dbsts, htgs (unfinished genomicsequences), gss, pdb, vector, mito, alu, epd1/29/08 CAP5510 24
Rules of Thumb Most sequences with significant similarity over their entirelengths are homologous. Matches that are > 50% identical in a 20-40 aa region occurfrequently by chance. Distantly related homologs may lack significant similarity.Homologous sequences may have few absolutely conservedresidues. A homologous to B & B to C A homologous to C. Low complexity regions, transmembrane regions and coiled-coilregions frequently display significant similarity withouthomology. Greater evolutionary distance implies that length of a localalignment required to achieve a statistically significant scorealso increases.1/29/08 CAP5510 25
Page 1 and 2: CAP 5510: Introduction to Bioinform
Page 3 and 4: Sequence Alignment - Why?>gi|126435
Page 5 and 6: Implications of Sequence AlignmentM
Page 7 and 8: PDGF and v-sis One region of 31 ami
Page 9 and 10: Sequence Alignment>gi|4505680|ref|N
Page 11 and 12: Similarity vs. HomologyHomologous s
Page 13 and 14: Types of Sequence Alignments - 2Sem
Page 15 and 16: Why gaps?Example: Finding the gene
Page 17 and 18: BLAST & FASTAFASTA[Lipman, Pearson
Page 19 and 20: BLAST Strategy & ImprovementsLipman
Page 21 and 22: BLAST Variants Nucleotide BLASTStan
Page 23: BLAST Credits Stephen Altschul Jona
Page 27 and 28: Types of Sequence AlignmentsGlobalH
Page 29 and 30: Global Alignment:An exampleV: G A A
Page 31 and 32: Alternative TracebackV: G - A A T T
Page 33 and 34: Improved TracebackGAATTCAGTTA000000
Page 36 and 37: Generalizations of Similarity Funct
Page 38 and 39: Local Sequence Alignment Example: c
Page 40 and 41: Local Alignment: ExampleGAATTCAGTTA
Page 42 and 43: How to score mismatches?1/29/08 CAP

Giri Narasimhan

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