BIOLOGICAL BIOLOGICAL DATABASESDATABASES

BIOLOGICAL DATABIOLOGICAL DATA• Bioinformatics is the science of Storing, Extracting,

Organizing, Analyzing, and Interpreting information in biological sequences

• Bioinformatics has been mainly fueled by advances in– DNA sequencing– Genome mapping techniques

• There are 3 billion base pairs that make up human DNA– Handling the massive amount of data is a challenge– Hence the necessity for Biological Databases

• Biological Data also includes protein sequences• The most famous example of the application of

bioinformatics and biological databases was the Human Genome Project

Data SourcesData Sources• Biological data can be of derived from a variety of

sources– Sequencing

• Analyzing DNA to find the exact sequence of nucleotides

• This method is used for the Human Genome Project

– Gene Expression• Determining which, previously known, genes are produced by a

specific organism

• One such way to detect expression is a Microarray– A synthetic chip to which certain DNA sequences will only bond to a

certain location– Allows for easy cataloging of genes produced by a specific organism

– Online Mendelian Inheritance in Man (OMIM)• Shows relations between diseases and any known responsible

genes within the human genome

DATA SUBMISSIONDATA SUBMISSION• Data storage is complicated

due to the wide array of sources and the need for cooperation and consistency amongst them

• Therefore, myriad methods have been implemented on resources such as the NCBI website

• To the right is a diagram showing the submission process for GenBank

DATASUBMISSION

NUCLEOTIDESEQUENCES

GENE EXPRESSIONOMNIBUS

EXPRESSION

GENBANK

BANKITSubmissions and

Updates via WWW

SEQUI NSubmissions and

Updates via SOFTWARE

A break down of Data Submission Process

EXTRACT AND EXTRACT AND ORGANIZE DATAORGANIZE DATA• Some of the databases are:

– Nucleotide• Contains nucleotide base pairs

– Taxonomy• Contains names of all organisms

that are in the genetic databases with at least one nucleotide or protein sequence

– Protein• Contains protein sequences

– OMIM • Online Mendelian Inheritance in

Man, a catalog of human genes and genetic diseases

DATABASES

LITERATURE DATABASES

PUBMEDPUBMED CENTRAL

OMIM

MOLECULAR DATABASES

NUCLEOTIDEPROTEIN

TAXONOMYSTRUCTURE

GENOMES

ENTREZ GENOMEMAP VIEWER

Some available databases

Diseases

OMIM

ANALYSIS TOOLSANALYSIS TOOLS• Biological data needs to be

analyzed to discover– Sequence structure– Functional patterns

• Existing databases contain ancillary information that may be of assistance to researchers/scientists

• Some Data Analyzing tools are:– BLAST

• Basic Local Alignment Search Tool• Similarity searches provide important clues to the function of uncharacterized proteins

– RasMol• Is an excellent and free molecular viewer available for Windows, Macintosh and UNIX

DATA ANALYSI STOOLS

SIMILARITY SEARCHING

NUCLEOTIDE SEQUENCEANALYSIS

PROTEIN SEQUENCEANALYSIS

MOLECULAR STRUCTUREANALYSIS