Giri Narasimhan

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Sequence AlignmentSequence 1 gi 332624 Simian sarcoma virus v-sis transformingprotein p28 gene, complete cds; and 3' LTR long terminal repeat,complete sequence. Length 2984 (1 .. 2984)Sequence 2 gi 4505680 Homo sapiens platelet-derived growth factorbeta polypeptide (simian sarcoma viral (v-sis) oncogene homolog)(PDGFB), transcript variant 1, mRNA Length 3373 (1 .. 3373)1/29/08 CAP5510 10
Similarity vs. HomologyHomologous sequences share commonancestry.Similar sequences are “near” to eachother by some appropriately definedmeasurable criteria.1/29/08 CAP5510 11
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: Sequence Alignment>gi|4505680|ref|N
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 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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