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Table 6.2. Web resources for performing database searches with a simple query sequence
Server/program   Web address or FTP site   References
BLAST—Basic Local Alignment Search Toola http://www.ncbi.nlm.nih.gov/BLAST
FTP to ftp.ncbi.nih.gov/blast/executables
Altschul et al. (1990, 1997);
Altschul and Gish (1996)
WU-BLASTb sites that run WU-BLAST 2.0 are listed at http://blast.wustl.edu
programs obtainable at http://blast.wustl.edu/blast/executables with licensing agreement
Altschul et al. (1990, 1997);
Altschul and Gish (1996)
FASTAc http://fasta.bioch.virginia.edu/fasta
FTP to ftp.virginia.edu/pub/fasta
Pearson (1995, 1996, 1998, 2000)
BCM Search Launcher (Baylor College of Medicine) http://searchlauncher.bcm.tmc.edu/ see Web site
TIGR gene indices search http://www.tigr.org see Web site
    There are also many other BLAST and FASTA servers on the Web, including ones for searches in specific organisms (see Chapter 11). The TIGR site is given as an example of such a site.
    a A stand-alone BLAST server may also be established on a local machine running Windows, UNIX, or Mac OS.
    b Executable programs for UNIX platforms are available from the FTP site.
    c Executable programs that run on PC, Macintosh, or UNIX platforms are available from the FTP site. The FASTA package also includes programs for performing pair-wise sequence alignments and for a statistical analysis of alignment scores (see Chapter 3). A number of Web sites offer FASTA database search, including the FASTA server and the BCM Search Launcher.

 

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