Web Sites providing on-line analytical programs

Numerous institutes and research centers provide access to analytical programs via web-pages. Many of these duplicate analyses that can be done easily with local programs such as GCG. However, under some circumstances, a web-site may offer an advantage, such as offering a simple interface to a program one is not familiar with yet, or access to customized databases better suited to your task then our local databases.

    Large sites (many programs):

    Institut Pasteur's Biological Software

    This is a large site with many programs. Some are limited to local users only, but most are publicly available via web-interfaces. There are several alignment programs, sequence format convertors, as well as excellent programs for evolutionary and phylogenetic studies, such as web-interfaces to PHYLIP programs, and FastDNAml and MOLPHY for maximum likelihood analysis of DNA and Protein sequences.

    SeWeR = Sequence analysis using WEB resources

    A Java application to provide interface and links to a collection of web-based programs for DNA and Protein analyses, hosted by Indiana University as well as several mirror sites (see bottom of SeWeR home page). You can choose to run SeWeR from one of the hosting sites, or just download the Java applet and run it in your own PC or Mac's web browser.

    ExPASy (Expert Protein Analysis System)

    The Proteomics server of the Swiss Institute of Bioinformatics (SIB). This server is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE (Disclaimer).

    Sequence alignment sites:

    ClustalW at EBI, Baylor College of Medicine, or GenomeNet (from Kyoto University)

    ClustalW is an excellent multiple alignment program, and several web-servers exist which can handle very large data sets. ClustalW is also available for PC's, Mac's and UNIX at numerous sites such as FinLand's CSC server, or Indiana University's FTP server.

    Colouring alignments for presentation:

    For those looking for alternative software for making colour alignments, try the web-based applications, Boxshade, or Cinema.

    examples of Cinema "mailback postscript" files - DNA - Protein

    Please email comments or suggestions about the ACHS MolBiol pages to mblack@virginia.edu.

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