- BLAST
- Choose from a variety of programs for comparing DNA or protein sequences
to NCBI databases
- COGnitor
- Search for Clusters of Orthologous Groups (COGS) of proteins in a complete genome
- DDBJ
- DNA Data Bank of Japan
- EcoCyc
- Search the genome and biochemical pathways of E. coli
- ExPASy Molecular Biology Server
- Compare proteins to a variety of databases
- KEGG
- The Kyoto Encyclopedia of Genes and Genomes
- MetaCyc
- A general biochemical pathway database
- PDB
- Protein Data Bank
- PIR
- Protein Information Resource
- Pfam
- Compare a protein sequence to multiple alignments and Hidden Markov Models
- Profile Scan (Motif Scan)
- Search for motifs in a sequence using Prosite and Pfam
- Prosite
- Search the ExPASy database of protein families and domains
- PSORT
- Prediction of protein localization sites in amino acid sequences
- SignalP
- Search for signal peptide cleavage sites in protein sequences
- Tandem Repeat Finder
- Locate tandem repeats in a FASTA
sequence
- TMHMM
- Prediction of transmembrane helices in proteins
- Unfinished
Microbial Genome Database
- BLAST against genome sequences not yet in GenBank
- Primer3 - Pick primers
from a DNA sequence
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- ACGT
- Bruce Roe's Advanced Center for Genome Technology at the University of Oklahoma Norman campus
- CSHL
- Cold Spring Harbor Laboratory in Cold Spring Harbor, NY
- EBI
- European Bioinformatics Institute in Cambridge, UK
- LANL
- Los Alamos National Laboratory in Los Alamos, NM
- NCBI
- National Center for Biotechnology Information
- Sanger Centre
- The Wellcome Trust Sanger Institute in Cambridge, UK
- Stein Laboratory
- Lincoln Stein's lab at CSHL
- TIGR
- The Institute for Genomic Research in Rockville, MD
- GSC
- Washington University Genome Sequencing Center in St. Louis
- *new* WinImp
- Free data compression/extraction software
- Artemis
- DNA sequence viewer and annotation tool
- Phred/Phrap/Consed
- A base-caller, assembler, and graphical editor
- TIGR software
- Various tools for analysis of eukaryotic and prokaryotic organisms
- Sanger software
- A large collection of sequence analysis software
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