Sites who provide www based services permit data entry by database accession number or "cut-paste" of your own sequence, usually in plain, continuous format without extra symbols (e;g; "fasta" format). So have your sequence ready in your Windows clipboard for pasting!

DATABASE SEARCHES AND RETRIEVAL (using keywords)

General Entrez searches (Sequences, Genomes, PubMed, Population data, PDB) and retrieval at NCBI-Genbank
Search dbEST, dbSTS, dbGSS general genome sequence databases.

Sequence Retrieval System (SRS) at EBI , EMBL, Sanger,  Inst. Pasteur (Paris), at ExPASy or choose from LIST
DBGET/LinkDB Integrated database retrieval system (Japan)
Search Swissprot/TREMBL - PROSITE (protein and patterns dictionary) databases
ProDOM and DOMO protein domain databases
Pfam Protein Families database at Sanger (UK) or UW (USA)
Enzyme and metabolic databases
VectorDB - Vector Database
Sequence databases at Inst. Pasteur (Paris)

BLAST SEARCHES WITH NUCLEOTIDE AND PEPTIDE SEQUENCES

BLAST Sequence Similarity Search (gapped blast and others) at NCBI.
Blast Searches at EMBnet-CH (includes TREMBL and others)
Search Parasite Genomes (EBI)
Search microbial genomes (NCBI)

GENERAL SEQUENCE ANALYSIS TOOLS AND SUPPORT

BioComputational Services and Tools at EMBL
Analyse your (hypothetical) gene and protein in-depth (Expasy and links)
Tools at the Institut Pasteur (Paris)
Alignments, frames, profiles etc. at EMBnet.CH
 
DEPOSIT OF SEQUENCES TO DATABASES

To Genbank
To dbEST
To dbSTS
To dbGSS
To EMBL

GENE FINDING AND CHARACTERIZATION

Find ORFs (NCBI)
Translate your nt sequence in hypothetical protein
Try different gene and exon predictions

PROTEIN STRUCTURE AND FUNCTION ANALYSIS

Expasy Protein databases (Swissprot; TREMBL), 2D and 3D data, PROSITE, enzyme nomenclature etc.
Expasy Protein characterization, structure analysis, similarity, pattern and profile searches etc.
NCBI Entrez 3D structure database and Protein Structure database.

BIOCHEMICAL PATHWAYS

Kegg metabolic pathways and searches
Boehringer Mannheim's Biochemical pathways
EcoCyc - E. coli genes and biochemical pathways
WIT metabolic reconstructions
Yeast biochemical pathways

SPECIAL SITES

Codon Tables
Graphical Codon Usage Analyser by Thomas Schoedl

PHYLOGENY SOFTWARE AND INFORMATION

The Tree of Life
Taxonomy at NCBI
Ribosomal Database Project
Treebase, a database of trees and phylogeny sources (Harvard)
Species2000, the world species index

IF YOU DID NOT FIND A SUITABLE LINK ON OUR SITE ...

The BioNetbook Web page directory for Biology
Amos' WWW links page
BioHunt Molecular Biology Finder
Expasy
EMBnet links to all individual member centers
DBCat, a catalog of databases
A Mol Biol Database list
General BioInformatics
Biopages at Harvard

FTP SITES FOR SOFTWARE AND DATABASES

Genbank database
EMBL database
Swissprot database
SANGER Center
NCBI : Sequence comparison software, contributed programs, Genbank, toolbox etc.
EMBOSS software suite (EMBL/Sanger)
A Bio-software index
Software for Unix, PC, Mac at Inst. Pasteur (Paris) or search the BioCatalog