Giri Narasimhan

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Why Gaps?Example: Aligning HIV sequences.Strain 1Strain 2Strain 3Strain 41/29/08 CAP5510 20
BLAST Variants Nucleotide BLASTStandard blastnMEGABLAST (Compare large sets, Near-exact searches)Short Sequences (higher E-value threshold, smaller word size, no low-complexityfiltering) Protein BLASTStandard blastpPSI-BLAST (Position Specific Iterated BLAST)PHI-BLAST (Pattern Hit Initiated BLAST; reg expr. Or Motif search)Short Sequences (higher E-value threshold, smaller word size, no low-complexityfiltering, PAM-30) Translating BLASTBlastx: Search nucleotide sequence in protein database (6 reading frames)Tblastn: Search protein sequence in nucleotide dBTblastx: Search nucleotide seq (6 frames) in nucleotide DB (6 frames)1/29/08 CAP5510 21
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: BLAST Strategy & ImprovementsLipman
Page 23 and 24: BLAST Credits Stephen Altschul Jona
Page 25 and 26: Rules of Thumb Most sequences with
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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