Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2003 Jul 1;31(13):3829-32.
doi: 10.1093/nar/gkg518.

PipeAlign: A new toolkit for protein family analysis

Frédéric Plewniak  1 , Laurent Bianchetti, Yann Brelivet, Annaick Carles, Frédéric 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
Affiliations

PipeAlign: A new toolkit for protein family analysis

Frédéric Plewniak et al. Nucleic Acids Res. .

Abstract

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/.

PubMed Disclaimer

Figures

Figure 1
Figure 1
The PipeAlign protein family analysis process.
Figure 2
Figure 2
Screenshots of a typical PipeAlign automa.
See this image and copyright information in PMC

References

    1. Lecompte O., Thompson,J.D., Plewniak,F., Thierry,J. and Poch,O. (2001) Multiple alignment of complete sequences (MACS) in the post-genomic era. Gene, 270, 17–30. - PubMed
    1. Plewniak F., Thompson,J.D. and Poch,O. (2000) Ballast: blast post-processing based on locally conserved segments. Bioinformatics, 9, 750–759. - PubMed
    1. Altschul S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 17, 3389–3402. - PMC - PubMed
    1. Thompson J.D., Plewniak,F., Thierry,J. and Poch,O. (2000) DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches. Nucleic Acids Res., 15, 2919–2926. - PMC - PubMed
    1. Thompson J.D., Plewniak,F., Thierry,J. and Poch,O. (2003) RASCAL: Rapid scanning and correction of multiple sequence alignment programs. Bioinformatics, in press. - PubMed

Publication types