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Chapter 3 Web Search Terms

Using dot matrix, sequence alignment, or pair-wise sequence alignment as search phrases is usually sufficient to find a current Web site with information, resources, or programs for performing pair-wise sequence alignment. A number of the more stable Web sites are shown in Table 3.1 and throughout the text. Often, a visit to the investigator's Web site will be fruitful. Some additional search terms are listed below.

BCM searchlauncher Baylor College of Medicine pair-wise sequence alignment on the Web.
DNA Strider A Macintosh suite of sequence analysis programs that includes dot matrix (see Marck 1988).
DOTTER Dot matrix using UNIX or Linux X-Window.
EMBOSS The European Molecular Biology Open Software Suite (EMBOSS) of programs that includes dot matrix and pair-wise sequence alignment programs. These must be run on the UNIX command line, but support is provided for building Web page interfaces (see Chapter 12).
FASTA University of Virginia sequence alignment on the Web using Pearson's FASTA suite.
PipMaker Alignment of long sequences and genomes on the Web with dot matrix-like display.
SSV Pair-wise chromosome viewer at Stanford University.


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