SAM (Sequence Alignment and Modeling) documentation

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# SAM
Sequence Alignment and Modeling
Software System

Richard Hughey

Kevin Karplus

Anders Krogh

sam-info@cse.ucsc.edu
Baskin Center for Computer Engineering and Science
University of California
Santa Cruz, CA 95064
Technical Report UCSC-CRL-99-11
Updated for SAM Version 3.4
July 31, 2003
Contributors:
Mark Diekhans, Leslie Grate
Christian Barrett, Michael Brown, Jonathan Casper, Melissa Cline,
Terry Figel, Rachel Karchin, Kimmen Sjölander, Christopher Tarnas
supersedes UCSC-CRL-95-07 and UCSC-CRL-96-22

### 概要:

The Sequence Alignment and Modeling system (SAM) is a collection of flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis. The model states can be viewed as representing the sequence of columns in a multiple sequence alignment, with provisions for arbitrary position-dependent insertions and deletions in each sequence. The models are trained on a family of protein or nucleic acid sequences using an expectation-maximization algorithm and a variety of algorithmic heuristics. A trained model can then be used to both generate multiple alignments and search databases for new members of the family.

SAM includes programs and scripts for the SAM-T2K method of remote homology detection. SAM-T2K is an iterative HMM search method for creating an HMM from a single protein sequence or seed alignment using iterative search of a protein database. The method is currently the most sensitive purely-sequence-based remote homology detection algorithm. SAM-T2K is based on successful methods created for the CASP2 and CASP3 protein structure prediction experiments.

The algorithms and methods used by SAM have been described in several pioneering papers from the University of California, Santa Cruz. These papers, as well as the SAM software suite, several servers, and links to related sites are available on the World-Wide Web to

`http://www.cse.ucsc.edu/research/compbio/sam.html`

- 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
    - 7.1.1 User-defined alphabets
    - 7.1.2 User-defined Numeric Alphabets
    - 7.1.3 Alphabet Background Files
  - 7.2 Sequences
  - 7.3 Models as sequences
  - 7.4 Training sets, test sets, and databases
- 8 Regularizers and models
  - 8.1 Regularizers
    - 8.1.1 Regularizer alternatives
    - 8.1.2 Transition regularizers with structural information
  - 8.2 Initial model
  - 8.3 Initial alignment
  - 8.4 Model format
    - 8.4.1 Model length
    - 8.4.2 Special nodes
    - 8.4.3 Node labels
    - 8.4.4 Codon models
    - 8.4.5 Binary models
  - 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
    - 9.2.1 Sequence-based Surgery
  - 9.3 Training statistics
  - 9.4 Weighted training
    - 9.4.1 External weighting
      - 9.4.1.1 Multi-subfamily weighting
    - 9.4.2 Annealing with Weights
    - 9.4.3 Internal weighting of alignments
    - 9.4.4 Internal weighting during training
  - 9.5 Viterbi training
  - 9.6 Global and semi-local training
  - 9.7 Building models with constraints
    - 9.7.1 Model Node Labels
    - 9.7.2 Constraints Definition File
    - 9.7.3 Using Constraints
  - 9.8 Reducing `buildmodel` runtime
- 10 Related programs
  - 10.1 `align2model` and `prettyalign`
    - 10.1.1 `prettyalign`
    - 10.1.2 Aligning fragments and SW
  - 10.2 `hmmscore`
    - 10.2.1 NLL-NULL scoring
    - 10.2.2 Reducing `hmmscore` runtime
    - 10.2.3 Selecting sequences, scores, and alignments
    - 10.2.4 Scoring Fragments
    - 10.2.5 Selecting multiple domain alignments
    - 10.2.6 Multi-track HMM scoring
    - 10.2.7 Distributed scoring
    - 10.2.8 Single Sequence Smith & Waterman Scoring and Alignment
    - 10.2.9 Scoring using the Kestrel parallel processor
    - 10.2.10 Calibration and Model libraries
  - 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
    - 10.10.1 `checkmodel`
    - 10.10.2 `drawmodel`
    - 10.10.3 `hmmconvert`
    - 10.10.4 `makelogo`
    - 10.10.5 `modifymodel`
    - 10.10.6 `sam2psi` and `psi2sam`
    - 10.10.7 Conversion between SAM and HMMer
      - 10.10.7.1 Internal HMM Structure
      - 10.10.7.2 Extra Information in HMMer
      - 10.10.7.3 Extra Information in SAM
  - 10.11 Plotting Programs
    - 10.11.1 `makehist`
    - 10.11.2 `makeroc`
    - 10.11.3 `makeroc2`
    - 10.11.4 `makeroc3`
  - 10.12 Sequence manipulation
    - 10.12.1 `listalphabets`
    - 10.12.2 `checkseq`
    - 10.12.3 `genseq`
    - 10.12.4 `permuteseq`
    - 10.12.5 `randseq`
    - 10.12.6 `splitseq`
    - 10.12.7 `sampleseqs`
    - 10.12.8 `sortseq`
    - 10.12.9 `uniqueseq`
    - 10.12.10 `mk_kestrel_db`
- 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
    - 11.5.1 Version 2.2.1
    - 11.5.2 Version 2.2
    - 11.5.3 Version 2.1.2
    - 11.5.4 Version 2.1.1
    - 11.5.5 Version 2.1
    - 11.5.6 Version 2.0
    - 11.5.7 Version 1.4
    - 11.5.8 Version 1.3
    - 11.5.9 Version 1.2
    - 11.5.10 Version 1.1
    - 11.5.11 Version 1.0
- 12 Parameter descriptions
- この文書について...

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