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Database Commons - GeneTack database

GeneTack database

Citations: 6

z-index 0.26

Short name GeneTack database
Full name GeneTack database
Description GeneTack database includes 206 991 fs-genes from 1106 complete prokaryotic genomes and 45 295 frameshifts predicted in mRNA sequences from 100 eukaryotic genomes.
URL http://topaz.gatech.edu/GeneTack/db.html
Year founded 2012
Last update & version 2012-11-17    
Availability Not Available
University/Institution hosted Georgia Institute of Technology
Address Atlanta,GA 30332,USA
City Atlanta
Province/State GA
Country/Region United States
Contact name Mark Borodovsky
Contact email borodovsky@gatech.edu
Data type(s)
Major organism(s)
Keyword(s)
  • fs-gene
Publication(s)
  • GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences. [PMID: 23161689]

    Ivan Antonov, Pavel Baranov, Mark Borodovsky
    Nucleic acids research 2013:41(Database issue)
    6 Citations (Google Scholar as of 2016-05-03)

    Abstract: Database annotations of prokaryotic genomes and eukaryotic mRNA sequences pay relatively low attention to frame transitions that disrupt protein-coding genes. Frame transitions (frameshifts) could be caused by sequencing errors or indel mutations inside protein-coding regions. Other observed frameshifts are related to recoding events (that evolved to control expression of some genes). Earlier, we have developed an algorithm and software program GeneTack for ab initio frameshift finding in intronless genes. Here, we describe a database (freely available at http://topaz.gatech.edu/GeneTack/db.html) containing genes with frameshifts (fs-genes) predicted by GeneTack. The database includes 206?991 fs-genes from 1106 complete prokaryotic genomes and 45?295 frameshifts predicted in mRNA sequences from 100 eukaryotic genomes. The whole set of fs-genes was grouped into clusters based on sequence similarity between fs-proteins (conceptually translated fs-genes), conservation of the frameshift position and frameshift direction (-1, +1). The fs-genes can be retrieved by similarity search to a given query sequence via a web interface, by fs-gene cluster browsing, etc. Clusters of fs-genes are characterized with respect to their likely origin, such as pseudogenization, phase variation, etc. The largest clusters contain fs-genes with programed frameshifts (related to recoding events).

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Tags

DNA Expression
Eukaryota Prokaryote
fs-gene

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Lin Liu [2016-03-29]
    • Lin Liu [2016-03-25]
    • Mengwei Li [2016-02-19]
    • Jian Sang [2015-12-05]
    • Jian Sang [2015-06-28]
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