What is bioinformatics?
Integrated use of computers and databases to store, analyze and interpret biological data.
Primarily thought of in the context of molecular genetic data (DNA sequence, mapping,
Is this really new (revolutionary) or just an evolutionary event in data processing?
Established technologies (still being improved)
How can you find available information about:
A gene's function?
A gene's structure?
A gene's location?
A gene's expression pattern?
Published papers on the gene?
Similar genes (and evolutionary relationships) in other species?
A specific chromosome?
Evolution across species
A specific organism?
Evolving bioinformatics technologies
Massively parallel gene expression studies- detecting co-regulated gene sets
SNP mapping data analysis and application to common disease gene mapping
Examples of bioinformatic analysis
Accession number: From publication on gene of interest, use Genbank nucleotide search
Gene or protein name: Text search of NCBI website (Genbank, PubMed, OMIM, Unigene)
Disease (human): Text search of OMIM
Researcher name: Text search of PubMed or Genbank
Sequence data: Begin with sequence of your clone, do comparison of your sequence
across available sequence information at NCBI website (BLAST (Genbank
nr, dbEST) to identify the sequence if possible.
If already cloned and sequenced, can determine the human and mouse
location (LocusLink, UniGene, GeneMap99, MGD-high probability of
location for known genes, many ESTs).
Also can find out what is known about gene (OMIM, PubMed, MXD)
Genbank flat file overview:
mRNA sequence flatfile example:
DNA sequence flatfile example:
Genbank Flat file contents
Locus line (accession number, length, type, sub-directory release date)
References to sequence
CDS (coding sequence) and conceptual translation
Miscellaneous features ( sig_peptide, polyA-signal, polymorphism)
Examples will be a) a high quality, full-length cDNA sequence and
b) a single-pass, incomplete sequence
Human Chromosome server (sorted by chromosome):
Mouse Genome database: http://www.informatics.jax.org/
Of interest: Genome database, Expression database, mammalian homologies
Pig Map/ BovMap/ Chickmap/Horse, etc: http://www.genome.iastate.edu/resources/other.html