Helix bioinformatics


	Context and situation

	Research activities

	Partnerships

	Teaching activities

	Members

	Former members


	Evolution of species and gene families

	Spatial organization of genomic information

	Syntaxic and functionnal genome annotation

	Proteomics

	Modeling and simulation of genetic regulatory networks

	Information extraction from texts


	Evolution of gene and gene families

	Spatial organization of genomic information

	Syntaxic and functionnal genome annotation

	Proteomics

	Modeling and simulation of genetic regulatory networks

	Information extraction from text


	Publications by year

	Publications by author

	Export


	The GenoStar integrated bioinformatics platform for exploratory genomics

	GEB: GenoExpertBacteria

	GNA: Genetic Network Analyzer

	PepLine: high throughput proteomics

	Herbs: checking the consistency of proteome annotations

	ISee: In Silico biology e-learning environment

	BOX: XML specifications of genomic data

	AROM: entity-relationship knowledge modeling


	Software and database releases

	Talks, seminars, poster presentations,...

	PhD and Master thesis defenses

	Training and job opportunities

What is bioinformatics?

A short introduction to bioinformatics

This introduction to bioinformatics, by François Rechenmann and Christian Gautier, has been published in the June 2000 issue of the french journal "La Recherche". The text has not been modified, although numerous scientific events and innovations have taken place since its publication.

It has been translated in English by Allison Quayle, at that time a student of Surrey University at Guilford (Great Britain), during the summer of the same year.

You can read this introduction online (see list of sections below) or download the text, complete with figures and inlets.


	The first genome projects
	The first complete genome of a living organism, the bacterium Haemophilus influenzae, was sequenced in July 1995

	Whole genome sequencing
	Sequencing a genome means finding out the sequence of nucleotides which make up the DNA macromolecule

	Genomic databases
	Part of the sequences is deposited in databanks which are freely accessible via the Internet.

	The problem of heterogeneous databases
	How can databases be reconciled when they are based on different definitions of a term as fundamental as 'gene'?

	Searching for homology through similarity of sequences
	A new sequence is immediately compared with those already held in banks and databases

	Finding genes in procaryotic genomes
	A prokaryotic genome is fairly dense and genes are continuous

	Finding genes in eucaryotic genomes
	Eukaryotic genes are made-up of coding exons and non-coding introns and are widely spaced out in the genome.

	Inferring gene functions from homology relationships
	Homologues, orthologues and paralogues

	The quest for gene fonction has not yet found an algorithmic solution
	Systematising tthe functionnal annotation process is a considerable challenge

	Modeling and simulating gene interaction networks and metabolic pathways
	From boolean networks to ambitious models linking the genomic and metabolic levels

	Biological data and knowlege need to be formalized
	The key issues in bioinformatics research are therefore not only to design powerful and appropriate algorithms, but also to provide tools which will make it easier to model, structure, query and visualise biological data and knowledge