PROMALS3D web server for accurate multiple protein sequence and structure alignments
نویسندگان
چکیده
Multiple sequence alignments are essential in computational sequence and structural analysis, with applications in homology detection, structure modeling, function prediction and phylogenetic analysis. We report PROMALS3D web server for constructing alignments for multiple protein sequences and/or structures using information from available 3D structures, database homologs and predicted secondary structures. PROMALS3D shows higher alignment accuracy than a number of other advanced methods. Input of PROMALS3D web server can be FASTA format protein sequences, PDB format protein structures and/or user-defined alignment constraints. The output page provides alignments with several formats, including a colored alignment augmented with useful information about sequence grouping, predicted secondary structures and consensus sequences. Intermediate results of sequence and structural database searches are also available. The PROMALS3D web server is available at: http://prodata.swmed.edu/promals3d/.
منابع مشابه
PROMALS3D: a tool for multiple protein sequence and structure alignments
Although multiple sequence alignments (MSAs) are essential for a wide range of applications from structure modeling to prediction of functional sites, construction of accurate MSAs for distantly related proteins remains a largely unsolved problem. The rapidly increasing database of spatial structures is a valuable source to improve alignment quality. We explore the use of 3D structural informat...
متن کاملPROMALS web server for accurate multiple protein sequence alignments
Multiple sequence alignments are essential in homology inference, structure modeling, functional prediction and phylogenetic analysis. We developed a web server that constructs multiple protein sequence alignments using PROMALS, a progressive method that improves alignment quality by using additional homologs from PSI-BLAST searches and secondary structure predictions from PSIPRED. PROMALS show...
متن کاملPROMALS: towards accurate multiple sequence alignments of distantly related proteins
MOTIVATION Accurate multiple sequence alignments are essential in protein structure modeling, functional prediction and efficient planning of experiments. Although the alignment problem has attracted considerable attention, preparation of high-quality alignments for distantly related sequences remains a difficult task. RESULTS We developed PROMALS, a multiple alignment method that shows promi...
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