CS262 Lecture 17, Win07, Batzoglou Gene Regulation and Microarrays.
CS273a Lecture 10, Aut 08, Batzoglou Multiple Sequence Alignment.
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273a Lecture 10, Aut 08, Batzoglou Multiple Sequence Alignment
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Transcript of CS273a Lecture 10, Aut 08, Batzoglou Multiple Sequence Alignment.
CS273a Lecture 10, Aut 08, Batzoglou
Multiple Sequence Alignment
CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
Evolution at the DNA level
…ACGGTGCAGTTACCA…
…AC----CAGTCCACCA…
Mutation
SEQUENCE EDITS
REARRANGEMENTS
Deletion
InversionTranslocationDuplication
CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
Orthology and Paralogy
HB HumanHB Human
WB WormWB Worm
HA1 HumanHA1 Human
HA2 HumanHA2 Human
YeastYeast
WA WormWA Worm
Orthologs:Derived by speciation
Paralogs:Everything else
CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
Orthology, Paralogy, Inparalogs, Outparalogs
CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
Genome Evolution – Macro Events
• Inversions• Deletions• Duplications
CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
Synteny maps
Comparison of human and mouse
CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
Synteny maps
CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
Synteny maps
CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
Synteny maps
CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
Building synteny maps
Recommended local aligners• BLASTZ
Most accurate, especially for genes Chains local alignments
• WU-BLAST Good tradeoff of efficiency/sensitivity Best command-line options
• BLAT Fast, less sensitive Good for
• comparing very similar sequences • finding rough homology map
CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
Index-based local alignment
Dictionary:
All words of length k (~10)
Alignment initiated between words of alignment score T
(typically T = k)
Alignment:
Ungapped extensions until score
below statistical threshold
Output:
All local alignments with score
> statistical threshold
……
……
query
DB
query
scan
Question: Using an idea from overlap detection, better way to find all local alignments between two genomes?
CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
Local Alignments
CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
After chaining
