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Contents
Contents
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Introduction to Version D 2.0
Related Programs
Background
Introduction
Needleman and Wunsch Algorithm
Predicting the likely quality of alignment
Multiple alignment strategy
Description of the AMPS package
MULTALIGN - Instructions for Use under Unix
Pairwise Alignment
Time considerations
Multiple Alignment Just using sequence information
Single order alignment
Tree based alignment
Comments
Multiple alignment - building on an existing alignment
Examples
Aligning without additional information
Secondary structure dependent gap_penalties
Defining explicit weights to align ONE extra sequence
Lookup tables
User Guide to the program ORDER
Flexible Pattern Matching and Database Scanning
Introduction
Program limits
Defining a Pattern
Defining the scoring scheme
Alternative scoring systems
Sorting the results of a scan using PROGRAM SORTER
To sort the output file and store the entire sorted list
To sort the output and store only the top N scoring results
Extracting the IDentifier codes for the top scoring sequences
Specifying a cutoff score
Generating Prolog Clauses
Generating a Histogram of the score distribution
Getting Help
Extracting Sequences from a PIR Database Using PROGRAM SELECT
Generating Alignments of the Pattern With Interesting Sequences
Generating multiple pattern alignments with each sequence
APPENDICES
Summary of Commands for MULTALIGN
MULTALIGN file formats
seq_file
matrix_file
order_file
tree_file
block_file
Save_lookup format
Format for Input to program PATT
VMS installation guide
Unix Installation Guide
Unix usage
References
Known Bugs
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