Prosite- A search tool for identifying domains/motifs in protein sequences.
National Center for Biotechnology Information (NCBI)- A variety of tools for sequence-based searchs, including BLAST, as well as access to Medline, the primary molecular biology literature database, via PubMed.
Baylor Search Launcher- Programs that evluate a genomic DNA sequence for a variety of important sequences (splicing, promoters, binding sites, etc).
Genefinder- Programs that splice genomic DNA into a predicted cDNA and predict the amino acid sequence of the encoded protein.
Pedro's Biomolecular Research Tools- A collection of dozens of useful links to web-based molecular biology resources.
Biocomputing Service Group- Links to a variety of gene prediction and analysis utilities, plus databases.