BLAST searches of NCBI's Non-redundant DNA & protein DBs, and dbEST BEAUTY (Blast Enhanced Alignment Utility); adds domain info to BLAST output FASTA-SWAP; FASTA-based pattern DB searches
For a comprehsensive list of freeware sequence analysis packages, see the Biocat Xgrail (Unix/X); X-windows interface to the client-server GRAIL system (exon/intron identification) Entrez (Mac, MS-Windows, and Unix/X network clients)
Keyword searches of GenBank, protein seq db's and MEDLINE abstracts;
also available via ftp GDE (Unix/X); multi-sequence alignment editor with direct access to alignment and phylogenetic
analysis programs (e.g., CLUSTAL-W, PHYLIP) SeqPup (Mac, MS-Windows, and Unix/X network clients); simple analysis package, includes Email server access also available via ftp
Sequence Submission Tools:
NCBI's Bank-it WWW submission form NCBI's Sequin (Mac; PC/Windows; Unix) for large or complex submissions, also available via ftp GSDB's Annotator (Mac; Unix)
BLAST review: S. Altschul et al.(1994)Nature Genetics 6:119-129.
Ancient conserved regions in gene sequences: P. Green (1994) Curr. Opin. Struct. Biol. 4:404-412.
Sequence Analysis Primer (M. Gribskov, J. Devereux, eds.) Stockton Press, 1991 (ISBN 0-333-
55092-7)
Geoff Barton's discussion of the issues in comparing protein sequences hypertext
UW Computer Science Department Algorithms in Molecular Biology Course postscript
Kim C. Worley Human Genome Center, Dept. of Molecular and Human Genetics, Baylor College of Medicine
kworley@bcm.tmc.edu; (713) 798-8292
