Bioinformatics lecture 2-- biological databases

examples of bioinformatics databases

1. Bibliographic (review articles/text)

2. Taxonomic (classification and taxonomy)

3. Nucleotides (sequences and genes)

4. genomic (complete genome per entery)

5. Protein (protein sequences/amino acids)

6. microarray/ gene expression (experiments, slides)

Why is bioinformatics important

1. keeping pace with information growth

2. knowledge discovery

3. data visualization

4. globalizing research

5. eliminating knowledge redundancy

types of biological information added

1. nucleic acids

2. proteins

3. Pathways

4. function

Nuclei acids

DNA sequences, genes, products (proteins), mutations, gene coding, distribution patterns, motifs

genomics: genome, gene structure expression, genetic map, genetics disorder

RNA sequences: secondary structure, 3D structure, interactions

Proteins:

protein sequences: corresponding gene, secondary structure, 3D structure, function, motifs, homology, interactions.

proteomics: expression profile, protein in disease processes

ligands and drugs: inhibitors, activators, substrates, and metabolites

Pathways

molecular networks (chain events, regulation, feedback, kinetic data

Function

Binding sites: interactions, molecular action (chem reactions, binding)

biological effects: signaling, transport, feedback, regulation, and modification

functional relationships: protein families, motifs, homologs

purpose of database

1. disseminate biological data and information

2. provide biological data in a computer readable form

3. allow analysis of biological data

T or F fatabas needs to have a minimum specific tool for searching and data extraction

True

T or F Web pages, books, journal articles, tables, text files, and spreadsheet files cannot be considered as databases

true

examples of objects in biology

1. sequences (nucs or aa)

2. topologies (extended sequences)

3. domains (functional units)

4. 3D structure (aided in data visualization)

5. Diagrams

6. 3D cartoons

Bibliographic databases

available in machine readable form in early 1960’s: medline and pubmed for mainly medical lit

exampl;es of bibliographical db

medline—- EBI

pubmed —-NCBI

embase——comercial prod

biosis—- old bio abstracts (broad field)

CAB—-agriculture and parasitic disease

Agricola—- the agri medline kinda

Taxonomic database

classification of all organisms, taxonomy browser is the most popular maintained by NCBI, is hierarchical and sequence based aims to centrilize the classification of all organisms in the databases with at least 1 nucleotide or protein sequence

Nucleotide databases

INSDC (international nucleotide sequence database collaboration is an joint op by EMBL(EBI)+DDBIJ (CIB)+GenBank(NCBI)

DDBJ, EMBL-BANK, GenBank

exchange new and updated data on a daily basis to achieve optimal synchronization

Genomic db

for geneticists

protein db

2 types:

1. simple archived sequence

2. annotated databases (additional info is added to a sequence record)

microarray and gene exp db

answer the question, What genes are expressed in a particular cell type of an organism, at a particular time and under particular conditions.

importance of a good neighborhood

deduction of a sequence using neighborly sequences

search engines

NCBI—-entrez

EBI —-SRS

CIBI—-getentry

types of databases

1. primary: raw, redundant, repository, by eperimentalists (genbank,emb,ddbj)

2. derivative/secondary: a) human cured

   b) computationallyh-derived

   c) combination

primary nuc sequence db

serve as a repository for scientist’s data, archival in nature, all sequence info