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Evaluating Sequence Alignments

MAS Saqi, PA Bates, MJE Sternberg. Towards an automatic method of predicting protein structure by homology An evaluation of suboptimal sequence alignments. Protein Eng 5 305-311, 1992. [Pg.347]

The ExPASy server (www.expasy.chl is one of the most useful servers, where almost any bioinforma tic tool can be found, together with useful links to other websites such as NCBI or EBI. The several access databases are descriptive, easy to follow, and up to date. Protein data bank searches with SwissProt or Trembl, as well as sequence alignments using either SimAlign (for two sequences) or ClustalW (for more than two protein sequences) can be started from ExPASy, to name just a few of the possibilities available. Access is also given to the Roche Applied Science Biochemical pathways where either keyword searches for particular enzymes or for metabolites can be performed, or entire metabolic pathways or sections thereof can be visualized. Proteomics evaluation is also available on ExPASy, which features free 2D-PAGE software called Melanie. [Pg.419]

Correction of the sequence alignment based on die evaluation of the model Iteration of the last three steps... [Pg.88]

Pairwise sequence alignments are typically evaluated through their constituent residue pairs. In this approach, each individual pair of residues is assigned a score, and the PSA is evaluated by summing the scores of all pairs (Figure 6.5). Because each position in the PSA is considered separately, every occurrence of the residue pair (a, b) receives the same score. Thus, for each possible (a, b) only one score... [Pg.87]

Knowledge of Three-Dimensional Structures Can Aid in the Evaluation of Sequence Alignments... [Pg.287]

Sequence (PSI-BLASTprofile) alignment with neural network based evaluation of alignments with structural scores... [Pg.295]

Hubbard, T. J., et al., SCOP, Structural Classification of Proteins database applications to evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data. Acta Crystallogr D Biol Crystallogr, 1998. 54(1 (Pt 6)) p. 1147-54. [Pg.315]

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Aligned sequence

Sequence alignment

Sequencing alignment

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