PROMALS web server for accurate multiple protein sequence alignments

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

Research output: Contribution to journalArticlepeer-review

58 Scopus citations


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:

Original languageEnglish (US)
Pages (from-to)W649-W652
JournalNucleic acids research
Issue numberSUPPL.2
StatePublished - Jul 2007

ASJC Scopus subject areas

  • Genetics


Dive into the research topics of 'PROMALS web server for accurate multiple protein sequence alignments'. Together they form a unique fingerprint.

Cite this