Giri Narasimhan

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BLAST Contd RPS BLASTCompare protein sequence against Conserved Domain DB; Helps in predictingrough structure and function Pairwise BLASTblastp (2 Proteins), blastn (2 nucleotides), tblastn (protein-nucleotide w/ 6frames), blastx (nucleotide-protein), tblastx (nucleotide w/6 framesnucleotidew/ 6 frames) Specialized BLASTHuman & Other finished/unfinished genomesP. falciparum: Search ESTs, STSs, GSSs, HTGsVecScreen: screen for contamination while sequencingIgBLAST: Immunoglobin sequence database1/29/08 CAP5510 22
BLAST Credits Stephen Altschul Jonathan Epstein David Lipman Tom Madden Scott McGinnis Jim Ostell Alex Schaffer Sergei Shavirin Heidi Sofia Jinghui Zhang1/29/08 CAP5510 23
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: BLAST Variants Nucleotide BLASTStan
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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