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Sequence Alignment and Modeling

Found one file extension association related to Sequence Alignment and Modeling and 1 file format developed specifically for use with Sequence Alignment and Modeling.

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Developer: Richard Hughey - Kevin Karplus - Anders Krogh

Richard Hughey - Kevin Karplus - Anders Krogh software list & details

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Sequence Alignment and Modeling

Developer / company: Richard Hughey - Kevin Karplus - Anders Krogh

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-T99 method of remote homology detection. SAM-T99 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-T99 is based on successful methods created for the CASP2 and CASP3 protein structure prediction experiments.

Sequence Alignment and Modeling works with the following file extensions:

Note: You can click on any file extension link from the list below, to view its detailed information. The list of extensions used or otherwise associated with the application may not be complete, because many common file extensions on our website, such as jpg (pictures) or txt (text files), can be opened by a large number of applications, or are too general file format. However most, if not all directly associated file extensions should be listed with its appropriate program. Although its likely, that some file extensions may be missing from the list of associated file extensions with the application, yet they can be opened, be part of, or otherwise be associated with the program.

Sequence Alignment and Modeling default file extension associations

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If you need more information please contact the developers of Sequence Alignment and Modeling (Richard Hughey - Kevin Karplus - Anders Krogh), or check out their product website.

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