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                -> GRAPH1...visualize conserved sequences in a multiple sequence alignment ? (last update May 9, 2006)

GRAPH1...visualize conserved sequences in a multiple sequence alignment ? (last update May 9, 2006)

For this purpose, the program Boxshade may be used. Boxshade is a program for pretty printing and shading of multiple alignment files. Boxshade includes several methods for coloring and boxing of multiple alignments. Note, that the alignment itself must be done using another program like ClustalW (see that question !). You may choose between several options at the Boxshade input page. If you chose "RTF_New" as output format, the boxed alignment can be directly opened in MS-WORD, and saved as a "normal" WORD-file. You may try different font sizes to see how that influences the overall size of the alignment (reidues per line). In addition, try different "fractions that must agree for shading", to see how the coloring changes. The "Input sequence format" should be set to "ALN" if you produced your alignment with ClustalW.

Jalview is a multiple alignment editor written in Java. It is used widely in a variety of web pages (e.g. the EBI ClustalW server and the Pfam protein domain database) but is available as a general purpose alignment editor. Jalview provides multiple options to sort and color multiple alignments. Note: If a ClustalW alignment is generated via the EBI web interface, a direct link to the Jalview display is automatically generated at the output page.