APPLICATIONS OF MULTIPLE ALIGNMENT
PPT Slide
MULTIPLE ALIGNMENT
Why do we search sequence databases?
Why run similarity searches?
Database searching doesn’t always find what we want…..
Biologically relevant sequences that are hard to find
How do we usually find them?
The bottom line …...
Scoring Matrices
A sample: Blosum62 Henikoff & Henikoff
Position Specific Scoring Matrix PSSM
Advantages of PSSM
Terminology
Terminology: Motif
Terminology: Pattern
Terminology: Profile
Search with a motif
Motifs Databases
Motifs in GCG
Search with a Consensus Pattern
Pattern length
FindPatterns in GCG
Searching special “pattern” databases
TransFac Database
Other available tools for patterns searches can be found on this page:
ProSite Database of Proteins families & domains
Prints Database
InterPro Database
Blocks database and tools
The BLOCKS web server
The BLOCKS Database
The Blocks Searcher tool
The Blocks Searcher
The Block Maker Tool
The Block Maker tool
COBBLER
PSI-BLAST
Producing the PSSM
Iteration
PHI-Blast
Email: shifra.ben-dor@weizmann.ac.il