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Contents
Contents
Wise2 Documentation (version 2.2 series)
Ewan Birney
EBI
Wellcome Trust Genome Campus
Contents
Overview
Authors
Introduction for the impatient
Common running modes
Common options to change
Common gripes, Cookbook and FAQ
It hasn't given me a complete gene prediction
How can I get rid of the annoying messages on stderr?
It goes far too slow
I have a new cosmid. What do I do?
Can I modify or use the Wise2 source code?
Making a single gene prediction on the basis of a close homolog
Using non human/worm/fly genomic DNA
Working with non spliced (bacterial) genomic DNA
Working with ESTs
Getting out the protein translation
Using Pfam
Optimising alignment speed
Optimising search speed
segmentation fault = bottle of champagne
Using GeneWise in a large scale throughput manner
Using EstWise in a large scale throughput manner
Installation
Building the executables
Environment set up
Building with thread support (for SMP machines)
Building Perl port
Concepts and conventions
Technical Approach
Introduction to Models in Wise2
Model
Parameterisation of the model
The protein model
Start End points
The gene model
The NULL model
Algorithms
Scores
Halfwise and Blastwise
Principle Programs
genewise
genewise - options: dna/protein
genewise - options: gene model
genewise - options: output
genewisedb
genewisedb - search modes
genewisedb - protein comparison options
genewisedb - gene model options
genewisedb output - for each comparison
genewisedb output - complete analysis
estwise
estwise - options: dna/protein
estwise - options: model
estwisedb
estwisedb - options: running modes
estwisedb - options: model
estwisedb - options: output
Running with pthreads
Other Programs
promoterwise
promoterwise - options
dba - Dna Block Aligner
dba - options
psw - Protein Smith-Waterman and other comparisons
psw - options
pswdb
psw - options
API
About this document ...
Eric DEVEAUD 2015-02-27
