PMID:14962936
| Citation |
Edgar, RC and Sjölander, K (2004) A comparison of scoring functions for protein sequence profile alignment. Bioinformatics 20:1301-8 |
|---|---|
| Abstract |
In recent years, several methods have been proposed for aligning two protein sequence profiles, with reported improvements in alignment accuracy and homolog discrimination versus sequence-sequence methods (e.g. BLAST) and profile-sequence methods (e.g. PSI-BLAST). Profile-profile alignment is also the iterated step in progressive multiple sequence alignment algorithms such as CLUSTALW. However, little is known about the relative performance of different profile-profile scoring functions. In this work, we evaluate the alignment accuracy of 23 different profile-profile scoring functions by comparing alignments of 488 pairs of sequences with identity < or =30% against structural alignments. We optimize parameters for all scoring functions on the same training set and use profiles of alignments from both PSI-BLAST and SAM-T99. Structural alignments are constructed from a consensus between the FSSP database and CE structural aligner. We compare the results with sequence-sequence and sequence-profile methods, including BLAST and PSI-BLAST. |
| Links |
PubMed Online version:10.1093/bioinformatics/bth090 |
| Keywords |
Algorithms; Amino Acid Sequence; Gene Expression Profiling/methods; Molecular Sequence Data; Reproducibility of Results; Sensitivity and Specificity; Sequence Alignment/methods; Sequence Analysis, Protein/methods; Sequence Homology, Amino Acid |
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