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1 Introduction
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SAM (Sequence Alignment and
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SAM (Sequence Alignment and
Contents
1 Introduction
1.1 Acknowledgments
2 New to this version
2.1 Version 3.3.1
2.2 Version 3.2.1
2.3 Version 3.2
2.4 Version 3.1
2.5 Version 3.0
3 Quick overview
3.1 Building a model
3.2 Aligning sequences
3.3 Examining models
3.4 Scoring sequences
3.5 Parameter selection
4 SAM-T99
4.1 SAM-T99 for superfamily modeling
4.2 Improved verification of homology
4.3 Family-level multiple alignments
4.4 Modeling non-contiguous domains
4.5 Building an HMM from a structural alignment
4.6 Improving existing multiple alignments
4.7 Creating a multiple alignment from unaligned sequences
4.8 Parameters for
target99
perl script
4.9 The model building scripts
4.10 Installing SAM-T99
4.11 SAM-T99 references
Bibliography
5 File types
6 Parameter specification
7 Sequence formats
7.1 Alphabets
7.2 Sequences
7.3 Training sets, test sets, and databases
8 Regularizers and models
8.1 Regularizers
8.2 Initial model
8.3 Initial alignment
8.4 Model format
8.5 Free-insertion modules
8.6 FIM, insert and match tables
9 The
buildmodel
estimation process
9.1 Noise and annealing
9.2 Surgery
9.3 Training statistics
9.4 Weighted training
9.5 Viterbi training
9.6 Building models with constraints
10 Related programs
10.1
align2model
and
prettyalign
10.2
hmmscore
10.3
addfims
10.4
grabdp
10.5
get_fisher_scores
10.6
modelfromalign
10.7
pathprobs
10.8
predict_track
10.9 Model manipulation
10.10 Plotting Programs
10.11 Sequence manipulation
11 System installation
11.1 Environment variables
11.2 Runtime statistics
11.3 Reducing runtime
11.4 Future Features
11.5 Prior versions
12 Parameter descriptions
About this document ...
SAM
sam-info@cse.ucsc.edu
UCSC Computational Biology Group
