Giri Narasimhan

More documents

Recommendations

Info

BLAST OverviewProgram(s) to search all sequence databasesTremendous Speed/Less SensitiveStatistical Significance reportedWWWBLAST, QBLAST (send now, retrieve resultslater), Standalone BLAST, BLASTcl3 (Clientversion, TCP/IP connection to NCBI server),BLAST URLAPI (to access QBLAST, no local client)1/29/08 CAP5510 18
BLAST Strategy & ImprovementsLipman et al.: speeded up finding “runs”of “hot spots”.Eugene Myers ’94: “Sublinear algorithmfor approximate keyword matching”.Karlin, Altschul, Dembo ’90, ’91:“Statistical Significance of Matches”1/29/08 CAP5510 19
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: BLAST & FASTAFASTA[Lipman, Pearson
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

Create successful ePaper yourself

Delete template?

Save as template?