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Contents
Contents
Introduction
Amino acid scoring schemes
Identity scoring
Genetic code scoring
Chemical similarity scoring
Observed substitutions
The Dayhoff mutation data matrix
PET91 - An updated Dayhoff matrix
BLOSUM - matrix from ungapped alignments.
Matrices derived from tertiary structure alignments
Which matrix should I use?
Comparison of two sequences
Sequence comparison without gaps - fixed length segments
Correlation methods
Variable length segments
Sequence comparison with gaps
Finding the best alignment with dynamic programming
Alternative weighting for gaps
Identification of local similarities
Finding second and subsequent best local alignments
Evaluation of alignment accuracy
Predicting overall alignment accuracy
Predicting quality using percentage identity
Predicting the reliable regions of an alignment
Incorporating non-sequence information into alignment
Multiple sequence alignment
Extension of dynamic programming to more than two sequences
Tree or hierarchical methods using dynamic programming
Extension of segment methods to multiple alignment
Representation and analysis of multiple alignments
Database scanning
Basic principles of database searching
Time considerations
Which database should I search? Local or network?
Searching with dynamic programming
Scanning with parallel computers Prosrch, MPsrch and others
Index methods
Simple index for identical matching
Indexing with gaps - the FLASH algorithm
Approximations: The FASTP and FASTA algorithm
Approximations: BLAST Basic Local Alignment Search Tool
Guidelines for Database Scanning
Summary
Figure Legends
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Figure 10
References
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