BIOINFORMATICS

The purpose of this page is to provide you with links for WWW based on-line nucleotide and protein sequence analysis, for database access, general information regarding bioinformatics including tutorials, and information about ftp sites for software download.
For Genomes and Genomics, see our GENOMICS pages.

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
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 unfinished 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
E. coli genes and biochemical pathways
WIT metabolic reconstructions
Yeast biochemical pathways

SPECIAL SITES

Codon Tables

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

BIOINFORMATICS AND COMPUTATIONAL BIOLOGY IN LATIN-AMERICA

Soon here : directory of research groups and people

TUTORIALS ON BIOINFORMATICS

BIOSCI/Bionet communications forum
BioInformatics guide for sequence analysis (Martin Aslett)
AAnP - IUPAC-IUBMB nomenclature for amino acids and peptides
Carbohydrates - IUPAC-IUBMB nomenclature for carbohydrates
Genetic codes - List of non-standard genetic codes from NCBI
Sequence similarity searches primer (Keith Robison, Harvard)
Pedestrian guide to analysing sequence databases (Rost and Schneider, EMBL)
Biocomputing courses resource list - Syllabi and tutorials on Bioinformatics (VSNS BCD)
Biocomputing tutorials - EMBnet Biocomputing tutorials
BioComputing Hypertext Coursebook - (VSNS BCD)
BioActivity - Protein sequence and structure analysis: a practical guide
Homology modeling course (EMBL)
BioInformatique, par SIS (Inst. Pasteur, Paris)

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
Bio-Access guide
Software for Unix, PC, Mac at Inst. Pasteur (Paris) or search the BioCatalog