PROMALS web server for accurate multiple protein sequence alignments

Jimin Pei, Bong Hyun Kim, Ming Tang, Nick V. Grishin

Research output: Contribution to journalArticle

51 Citations (Scopus)

Abstract

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 shows higher alignment accuracy than other advanced methods, such as MUMMALS, ProbCons, MAFFT and SPEM. The PROMALS web server takes FASTA format protein sequences as input. The output includes a colored alignment augmented with information about sequence grouping, predicted secondary structures and positional conservation. The PROMALS web server is available at: http://prodata.swmed.edu/promals/.

Original languageEnglish (US)
JournalNucleic Acids Research
Volume35
Issue numberSUPPL.2
DOIs
StatePublished - Jul 2007

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Sequence Alignment
Proteins

ASJC Scopus subject areas

  • Genetics

Cite this

PROMALS web server for accurate multiple protein sequence alignments. / Pei, Jimin; Kim, Bong Hyun; Tang, Ming; Grishin, Nick V.

In: Nucleic Acids Research, Vol. 35, No. SUPPL.2, 07.2007.

Research output: Contribution to journalArticle

Pei, Jimin ; Kim, Bong Hyun ; Tang, Ming ; Grishin, Nick V. / PROMALS web server for accurate multiple protein sequence alignments. In: Nucleic Acids Research. 2007 ; Vol. 35, No. SUPPL.2.
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