Multifunctional Tools

EMBOSS - A comprehensive set of sequence analysis programs that handles all sequence formats (NIH only)
NIH EMBOSS-lite - interface to the more popular EMBOSS utilities (NIH only)
NIAID BioCluster: Bioinformatics Portal - Access to 200 bioinformatics applications and custom workflows using a convenient web-based interface (NIH only)
ABS - Analytical Biostatics Section (NIH only)
DAVID - Database for Annotation, Visualization and Integrated Discovery (NIH only)
EBI Services - EMBL European Bioinformatics Institute Services
EMBL Heidelberg Tools - EMBL Heidelberg
MannDB - Protein sequence analysis of microbial databases, at LLNL
Institute for Genomics and Bioinformatics - Structural Proteomics

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
PDB Searches - advanced search at the PDB
Nucleic Acid Database Search - at Rutgers
Annotation-Modules - tool for finding significant combinations of multisource annotations, at CIC bioGUNE
PDBsum - At-a-glance overview of PDB structures, at EBI

Sequence Format Conversion

Format Conversion via EMBOSS seqret - at Helix Systems (NIH only)
READSEQ Sequence Conversion - at CIT/NIH

Database Similiarity/Homology Searches

Basic Local Alignment Search Tool (BLAST) - the gold standard for homology searches
Parallel Fasta for Proteins - very fast homology search of databases at Helix Systems (NIH only)
Fasta3 Database Search - variants of fasta at EBI

Sequence Alignments

Multiple Alignment Workshop - Calculate & compare multiple sequence alignments (NIH only)
EMBOSS sequence comparison tools - at Helix Systems (NIH only)
PROMALS3D - constructs alignments for multiple protein sequences and/or structures, at Southwestern Medical Center at Dallas
FAST - Fourier transform based multiple sequence alignment, at Cornell Univ.
PRALINE - Multiple sequence alignment of transmembrane proteins, at Amsterdam Univ.
Exalign - Align exon and intron sequences against multiple databases, at Univ. of Bari
ConSequenceS - Generate consensus sequences from multiple sequence alignment, at Columbia University

Restriction Enzyme Analysis

EMBOSS Map/MapSort Programs - GCG utility for DNA digest analysis, at Helix Sytems (NIH only)
Webcutter (v2.0) - Maxwell Heiman's popular web-based restriction digest program
PlasMapper (v2.0) - generate annotated circular plasmid maps, David Wishart, U. Alberta, CA

Pattern Matching

Prosite Database Search - at EBI
EMBOSS patmatmotifs - (equivalent to GCG Motifs) at Helix Systems (NIH only)
Promoter Scan - at CIT/NIH
Signal Scan - at CIT/NIH
AIMIE - discover and interpret sequence motifs in prokaryotic genomes, at UGA

Protein Sequence Analysis

EMBOSS-Lite - Protein Sequence Analysis - at Helix Systems (NIH only)
Statistical Analysis of Protein Sequences (SAPS) - at Helix Systems (NIH only)
ExPASy Proteomics Tools - massive collection of utilities at ExPASy.org
Pratt - search for patterns conserved in sets of unaligned protein sequences, at EBI
ProteinProspector - tools for mining sequence databases in conjunction with MS experiments
FFAS03 - profile-profile alignments and fold family of a sequence, The Burnham Institute
DISTILL - suite of web-servers for the prediction of protein structures, University College Dublin
ProFAT - tool for the functional annotation of proteins via the detection of weak homologies, Max Planck Institute of Molecular Cell Biology and Genetics
GeneTools - collection of resources for functional annotations, Norwegian University of Science and Technology
ConFunc - Conserved residue Protein Function Prediction Server, at Imperial College London
Swelfe - A tool to detect internal repeats in DNA and amino acid sequences and in 3D structures, at RPBS
ProBias - identification of user-specified types of compositionally biased segments in protein sequences, at Univ. of Albany
PFP - predict GO annotations for a query protein sequence, at Purdue Univ.
MetalDetector - classifies histidines and cysteines in a sequence into free, metal-bound, or disulfide, at Univ. Firenze

Nucleic Acid Sequence Analysis

EMBOSS-Lite - DNA Sequence Analysis - at Helix Systems (NIH only)
MFOLD Web Interface - at Helix Systems (NIH only)
RDMAS - RNA Deleterious Mutation Analysis, at Beijing Inst. of Radiation Medicine
Mireval - Prediction of microRNA in genome sequences, at INSERM
nuScore - Deformation energy and nucleosome-positioning score calculator, at Harvard Univ.
iFoldRNA - Three dimensional RNA structure prediction and folding, at Univ. North Carolina

Phylogentics and Linkage Analysis

PhyloWidget - for viewing, editing, and publishing phylogenetic trees, from Google Summer of Code

Synthesis

DNAWorks - automatic oligonucleotide design for gene synthesis, at Helix Systems
MOSAIC - design and assess vaccine candidate protein sequences, at LLNL

Visualization

GenomeVx - Generate circular chromosome maps, at Trinity College