SFESA: a web server for pairwise alignment refinement by secondary structure shifts.
BACKGROUND
Protein sequence alignment is essential for a variety of tasks such as homology modeling and active site prediction. Alignment errors remain the main cause of low-quality structure models. A bioinformatics tool to refine alignments is needed to make protein alignments more accurate.


RESULTS
We developed the SFESA web server to refine pairwise protein sequence alignments. Compared to the previous version of SFESA, which required a set of 3D coordinates for a protein, the new server will search a sequence database for the closest homolog with an available 3D structure to be used as a template. For each alignment block defined by secondary structure elements in the template, SFESA evaluates alignment variants generated by local shifts and selects the best-scoring alignment variant. A scoring function that combines the sequence score of profile-profile comparison and the structure score of template-derived contact energy is used for evaluation of alignments. PROMALS pairwise alignments refined by SFESA are more accurate than those produced by current advanced alignment methods such as HHpred and CNFpred. In addition, SFESA also improves alignments generated by other software.


CONCLUSIONS
SFESA is a web-based tool for alignment refinement, designed for researchers to compute, refine, and evaluate pairwise alignments with a combined sequence and structure scoring of alignment blocks. To our knowledge, the SFESA web server is the only tool that refines alignments by evaluating local shifts of secondary structure elements. The SFESA web server is available at http://prodata.swmed.edu/sfesa.
Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, TX, 75390-9050, USA. jing.tong@utsouthwestern.edu.
Jing
J
Tong
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, TX, 75390-9050, USA. jpei@chop.swmed.edu.
Jimin
J
Pei
Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, TX, 75390-9050, USA. grishin@chop.swmed.edu.|Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, TX, 75390-9050, USA. grishin@chop.swmed.edu.
Nick V
NV
Grishin
D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D030561:Databases, Nucleic Acid; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*
D011506:Proteins