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Sequence Alignment and Modeling System (SAM) UC, Stata Cruz.

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Presentation on theme: "Sequence Alignment and Modeling System (SAM) UC, Stata Cruz."— Presentation transcript:

1 Sequence Alignment and Modeling System (SAM) UC, Stata Cruz

2 Quick Overview What is can do? Modeling, aligning and discriminating biological sequences (DNA, RNA, protein) Given A set of biological sequences (regard as ‘related’) SAM-T2K This method is available in SAM 3.0 or higher, used to build a linear HMM representing the given set

3 Linear HMM The model is a linear sequence of nodes, including match (square), insert (diamond) and delete (circle)

4 Applications and Contributions Protein structure prediction It is also an Automatic entries to CASP5 (SAM-T99, SAM-T02) and CASP4 (SAM-T99) Yeast (S. cerervisiae) protein predictions SCOP super-family search and alignment library (not work now) Program update SAM-T98  SAM-T99  SAM-T02 22 publications

5 CASP Critical Assessment of techniques for Protein Structure Prediction Once 2 years CASP1 (1994) CASP2 (1996) CASP3 (1998) CASP4 (2000) CASP5 (2002) CASP6 (2004) CASP7 (2006), coming soon!

6 Program Structure (version 3.5) Test set Related sequences Aligned sequences modelfromalign buildmodel Library of aa distribution Preliminary model Evaluate HMM model align2modelhmmscore Protein DB Refine model Fine-tuned HMM model (1) (2) (3) (1) (2) MSA resultsPossible members

7 Primary programs Build a model buildmodel (from unaligned sequences) modelfromalign (from aligned sequences) Exeaming models makelogo and drawmodel Perform MSA align2model and prettyalign Scoring Sequences hmmscore Choose ‘significant’ sequence entries by 2 scores target2k Use one sequence as ‘seed’ to iteratively create model

8 Assignment Data Obtain a set of close related sequences, split into 2 parts: training and testing Hint: check known protein families Procedure Build a model for training set Evaluate the model by testing set Search all possible via HMM-based DB search Multiple alignment ‘given’ and ‘found’ Please read sam_doc.pdf (full manual)


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