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BLOSUM62 Matrix
Lecture2/lect9b/bovmg.seq
Lecture2/lect9b/bovmg.pair.txt
Lecture2/lect9b/cowmyo.pep
Lecture2/lect9b/fishdna.pair.txt
Lecture2/lect9b/fishmyo.pair.txt
Lecture2/lect9b/fishmyo.pep
Lecture2/lect9b/fishmyo.seq
Lecture2/lect9b/pigmg.seq
Lecture2/lect9b/pigmyo.pep
BLOSUM62 Substitution Matrix

ALIGNMENT

9/26/98


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Table of Contents

ALIGNMENT

Alignments

Alignments

Origins of Sequence Similarity

Similarity

Mismatches

Terminal Mismatch

INDELS

Indels, cont’d

Similarity Scoring

DNA Scoring

Absurdity of Low Gap Penalty

Algorithms

Programs

BESTFIT vs GAP

Statistical Significance

Program Limitations

Protein Similarity

Single-Base Evolution

Substitution Matrices

PAM-Dayhoff

BLOSUM-Henikoff&Henikoff

BLOSUM62

BLOSUM62-2

Gaps

Alignment Statistics

“Real” Alignments

Real Alignments

Phylogeny

Cow-to-Pig

Cow-to-Pig cDNA

DNA similarity reflects polypeptide similarity

Coding vs Non-coding Regions

Third Base of Codon Hypervariable

Cow-to-Fish Protein

Cow-to-Fish DNA

Protein vs DNA Alignments

Author: cstaben

Email: staben@pop.uky.edu

Home Page: www.uky.edu/Classes/BIO520/BIO520WWW/

Other information:
Lab 5 due Wednesday, 9/30 USE RASMOL 2.6! Download it to the lab Macs! Sign onto the listserv! Fall Break is Oct.2-no assignment

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University of KentuckyMorgan School of Biological SciencesNSF-CCD Support wpe1.jpg (5798 bytes)Chuck Staben, copyright reserved || 10/09/98