PipeAlign: A new toolkit for protein family analysis

Frádáric Plewniak, Laurent Bianchetti, Yann Brelivet, Annaick Carles, Frádáric Chalmel, Odile Lecompte, Thiebaut Mochel, Luc Moulinier, Arnaud Muller, Jean Muller, Veronique Prigent, Raymond Ripp, Jean Claude Thierry, Julie D. Thompson, Nicolas Wicker, Olivier Poch*

*Corresponding author for this work

Research output: Contribution to journalArticleResearchpeer-review

104 Citations (Scopus)


PipeAlign is a protein family analysis tool integrating a five step process ranging from the search for sequence homologues in protein and 3D structure databases to the definition of the hierarchical relationships within and between subfamilies. The complete, automatic pipeline takes a single sequence or a set of sequences as input and constructs a high-quality, validated MACS (multiple alignment of complete sequences) in which sequences are clustered into potential functional subgroups. For the more experienced user, the PipeAlign server also provides numerous options to run only a part of the analysis, with the possibility to modify the default parameters of each software module. For example, the user can choose to enter an existing multiple sequence alignment for refinement, validation and subsequent clustering of the sequences. The aim is to provide an interactive workbench for the validation, integration and presentation of a protein family, not only at the sequence level, but also at the structural and functional levels. PipeAlign is available at http://igbmc.u-strasbg.fr/PipeAlign/.

Original languageEnglish
Pages (from-to)3829-3832
Number of pages4
JournalNucleic Acids Research
Issue number13
Publication statusPublished - 1 Jul 2003
Externally publishedYes


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