BINF 511 Lecture Notes - Lecture 4: Ford Probe, Unique Key, Medical Subject Headings (Mesh)
25 Jun 2018
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Lecture 4B: NCBI/GenBank
January 31, 2018
NCBI (National Center for Biotechnology Information)
Home to biological data bases (GenBank), literature (PubMed), and sequence tools (BLAST)
HomoloGene
oPairwise orthologs
o20 completed genomes
o"An automated system for constructing putative homology groups from the complete
gene sets of a wide range of eukaryotic species"
oDefinitions
Homolog
Same gene in different genomes/organisms
A gene related to a second gene by descent from a common ancestral
DNA sequence
Ortholog
Homologous genes from different organisms that diverged by speciation
In other words, orthologs are genes in different species that evolved
from a common ancestral gene by speciation; orthologs retain the same
function in the course of evolution
Paralog:
Homologous genes that have diverged by gene duplications
In other words, paralog genes are related by duplication within a
genome. However, paralogs evolve new functions, even if these are related to
the original one
NCBI: Gene Express Omnibus (GEO)
oFor gene expression (microarray) data
GenBank
Three sequence banks in one (GenBank/EMBL/DDBJ)
oPart of a larger worldwide collaboration (International Nucleotide Sequence Database
Collaboration (INSDC))
oEMBL is from Europe
oDDBJ is from Japan
oIf you add information to one database, the others will automatically be updated
Divisions by sequence type, divisions by taxonomy
Many databases (divisions) in one, can search different combinations of databases
GenBank record
oOrganized in a relational database
oThe GenBank Flat File
Header content - locus line
Locus name, length of sequence, type of molecule, division code, date
published
Header content - definition line
Genus species product name, summary of the biology of the record,
appears in the FASTA files generated by NCBI, information seen when BLAST
search is generated
Header content - accession number
find more resources at oneclass.com
find more resources at oneclass.com
Document Summary
Home to biological data bases (genbank), literature (pubmed), and sequence tools (blast) "an automated system for constructing putative homology groups from the complete gene sets of a wide range of eukaryotic species: definitions. A gene related to a second gene by descent from a common ancestral. Homologous genes from different organisms that diverged by speciation. In other words, orthologs are genes in different species that evolved from a common ancestral gene by speciation; orthologs retain the same function in the course of evolution. Homologous genes that have diverged by gene duplications. In other words, paralog genes are related by duplication within a genome. However, paralogs evolve new functions, even if these are related to the original one. Three sequence banks in one (genbank/embl/ddbj) o. Part of a larger worldwide collaboration (international nucleotide sequence database. Embl is from europe: ddbj is from japan o. If you add information to one database, the others will automatically be updated.
