:
1 Introduction
:
SAM (Sequence Alignment and
:
SAM (Sequence Alignment and
目次
1 Introduction
1.1 Acknowledgments
2 New to this version
2.1 Version 3.5
2.2 Version 3.4
2.3 Version 3.3.2
2.4 Version 3.3.1
2.5 Version 3.2.1
2.6 Version 3.2
2.7 Version 3.1
2.8 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-T2K
4.1 SAM-T2K 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 target2k perl script
4.9 The model building scripts
4.10 Support scripts
4.11 Installing SAM-T2K
4.12 SAM-T2K references
参考文献
5 File types
6 Parameter specification
7 Sequence formats
7.1 Alphabets
7.2 Sequences
7.3 Models as sequences
7.4 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 Frequency-based Surgery
9.3 Training statistics
9.4 Weighted training
9.5 Viterbi training
9.6 Global and semi-local training
9.7 Building models with constraints
9.8 Reducing buildmodel runtime
10 Related programs
10.1 align2model and prettyalign
10.2 hmmscore
10.3 addfims
10.4 fragfinder
10.5 grabdp
10.6 get_fisher_scores
10.7 modelfromalign
10.8 pathprobs
10.9 predict_track
10.10 Model manipulation
10.11 Plotting Programs
10.12 Sequence manipulation
11 System installation
11.1 Environment variables
11.2 Runtime statistics
11.3 Manipulating large collections of data
11.4 Future Features
11.5 Prior versions
12 Parameter descriptions
SAM
sam-info@cse.ucsc.edu
UCSC Computational Biology Group
