Multifunctional Tools
EBI Services - EMBL European Bioinformatics Institute Services
BCM Search Launcher - Baylor College of Medicine HGSC
CMS Molecular Biology Resource - Dr. Smith (University of California)
EMBL Heidelberg Tools - EMBL Heidelberg

Text-Based Query of Sequence Databases
Entrez Cross Database Query - one-stop shopping for NCBI databases
Sequence Retreival System - at EBI (UniProt)
SwissProt Search - at ExPASy.org (UniProt)
PIR Searches - at Georgetown University (UniProt)
Molecules To Go - text-based interface to the PDB on Helix Systems
Nucleic Acid Database Search - at Rutgers

Sequence Format Conversion
READSEQ Sequence Conversion - at CIT/NIH

Database Similiarity/Homology Searches
Basic Local Alignment Search Tool (BLAST) - homology searches
Fasta3 Database Search - variants of fasta at EBI

Sequence Alignments
Multiple Alignment Workshop - Calculate & compare multiple sequence alignments

Restriction Enzyme Analysis
Webcutter (v2.0) - Maxwell Heiman's popular web-based restriction digest program
PlasMapper (v2.0) - generate annotated circular plasmid maps, David Wishart

Pattern Matching
Prosite Database Search - at EBI
Promoter Scan - at CIT/NIH
Signal Scan - at CIT/NIH