Web Sites That Provide Online Analytical Programs

[Nov 23, 2009 14:09] Web access to Microsoft Live@edu accounts now works.

Many institutes and research centers provide access to analytical programs via Web pages. Many of these are 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 a simple interface to a program one is not yet familiar with, or access to customized databases better suited to your task then our local databases.

Herewith, we offer a list of such Web-based resources hosted by other institutions.

Large Sites

  • 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, and 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. This is a Java application that provides 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 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, available at EBI, Baylor College of Medicine, or GenomeNet (from Kyoto University), is an excellent multiple alignment program. Several Web servers exist that can handle very large data sets. ClustalW is also available for PCs, Macs, and UNIX, and can be downloaded via the EBI web site. Note that ClustalW is the command line version, while ClustalX is the graphical version for Windows and Mac. You do not need both.

Colouring Alignments for Presentation

Those looking for alternative software for making colour alignments can try the Web-based applications, Boxshade and Cinema. Examples Cinema "mailback postscript" files: DNA | Protein.

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