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bioinformatics-451-2004

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					                                       Bioinformatics

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,
       expression, etc.).

       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?

       Chromosome structure

       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


Starting material:

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

Genbank flat file overview:

mRNA sequence flatfile example:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=Retrieve&list_uids=
2306974&dopt=GenBank

DNA sequence flatfile example:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=Retrieve&list_uids=
451311&dopt=GenBank

Genbank Flat file contents
             Locus line (accession number, length, type, sub-directory release date)
             Definition Line
             Accession number
             Version
             Keywords
             Source
             References to sequence
             Features Table
                      Source
                      Gene
                      CDS (coding sequence) and conceptual translation
                      Miscellaneous features ( sig_peptide, polyA-signal, polymorphism)
                Base Count
                Sequence



BLAST analyses:

Examples will be              a) a high quality, full-length cDNA sequence and
                              b) a single-pass, incomplete sequence

Useful sites:

                NCBI      http://www.ncbi.nlm.nih.gov/
                BLAST:    http://www.ncbi.nlm.nih.gov/BLAST/
                GENEMAP: http://www.ncbi.nlm.nih.gov/genemap99/
                PUBMED:   http://www.ncbi.nlm.nih.gov/entrez/query.fcgi
                OMIM:     http://www.ncbi.nlm.nih.gov/omim/
                UNIGENE: http://www.ncbi.nlm.nih.gov/omim/
                LOCUSLINK:http://www.ncbi.nlm.nih.gov/LocusLink/
                HOMOLOGY: http://www.ncbi.nlm.nih.gov/Homology/


Human Chromosome server (sorted by chromosome):
                                       http://www.ornl.gov/hgmis/launchpad/

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

				
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