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Database Commons - OrtholugeDB

OrtholugeDB

Citations: 17

z-index 3.37

Short name OrtholugeDB
Full name A Bacterial and Archaeal Orthology Resource
Description OrtholugeDB contains Ortholuge-based orthology predictions for completely sequenced bacterial and archaeal genomes.
URL http://www.pathogenomics.sfu.ca/ortholugedb/
Year founded 2012
Last update & version 2012-11-29    v2.0
Availability Free to all users
University/Institution hosted Simon Fraser University
Address Burnaby,British Columbia V5A 1S6,Canada
City Burnaby
Province/State British Columbia
Country/Region Canada
Contact name Fiona S. L. Brinkman
Contact email brinkman@sfu.ca
Data type(s)
Major organism(s)
Keyword(s)
  • orthology
Publication(s)
  • OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis. [PMID: 23203876]

    Matthew D Whiteside, Geoffrey L Winsor, Matthew R Laird, Fiona S L Brinkman
    Nucleic acids research 2013:41(Database issue)
    17 Citations (Google Scholar as of 2016-01-14)

    Abstract: Prediction of orthologs (homologous genes that diverged because of speciation) is an integral component of many comparative genomics methods. Although orthologs are more likely to have similar function versus paralogs (genes that diverged because of duplication), recent studies have shown that their degree of functional conservation is variable. Also, there are inherent problems with several large-scale ortholog prediction approaches. To address these issues, we previously developed Ortholuge, which uses phylogenetic distance ratios to provide more precise ortholog assessments for a set of predicted orthologs. However, the original version of Ortholuge required manual intervention and was not easily accessible; therefore, we now report the development of OrtholugeDB, available online at http://www.pathogenomics.sfu.ca/ortholugedb. OrtholugeDB provides ortholog predictions for completely sequenced bacterial and archaeal genomes from NCBI based on reciprocal best Basic Local Alignment Search Tool hits, supplemented with further evaluation by the more precise Ortholuge method. The OrtholugeDB web interface facilitates user-friendly and flexible ortholog analysis, from single genes to genomes, plus flexible data download options. We compare Ortholuge with similar methods, showing how it may more consistently identify orthologs with conserved features across a wide range of taxonomic distances. OrtholugeDB facilitates rapid, and more accurate, bacterial and archaeal comparative genomic analysis and large-scale ortholog predictions.

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Accessibility

Rate of accessibility:
HTTP status codeDate requested
200 OK2018-11-16
200 OK2018-11-13
200 OK2018-11-09
200 OK2018-11-06
200 OK2018-11-02
200 OK2018-10-30
200 OK2018-10-26
200 OK2018-10-23
200 OK2018-10-19
200 OK2018-10-16
200 OK2018-10-12
200 OK2018-10-09
200 OK2018-10-05
200 OK2018-10-02
200 OK2018-09-28
200 OK2018-09-25
200 OK2018-09-21
200 OK2018-09-18
200 OK2018-09-14
200 OK2018-09-11
200 OK2018-09-07
200 OK2018-09-04
200 OK2018-08-31
200 OK2018-08-28
200 OK2018-08-24
200 OK2018-08-21
200 OK2018-08-17
200 OK2018-08-14
200 OK2018-08-10
200 OK2018-08-07
200 OK2018-08-03
200 OK2018-07-31
200 OK2018-07-27
200 OK2018-07-24
200 OK2018-07-20
200 OK2018-07-17
200 OK2018-07-13
200 OK2018-07-10
200 OK2018-07-06
200 OK2018-07-03
200 OK2018-06-29
200 OK2018-06-26
200 OK2018-06-22
200 OK2018-06-19
200 OK2018-06-15
200 OK2018-06-12
200 OK2018-06-08
200 OK2018-06-05
200 OK2018-06-01
200 OK2018-05-29
200 OK2018-05-25
200 OK2018-05-22
200 OK2018-05-18
200 OK2018-05-15
200 OK2018-05-11
200 OK2018-05-08
200 OK2018-05-04
200 OK2018-05-01
200 OK2018-04-27
200 OK2018-04-24
200 OK2018-04-20
200 OK2018-04-17
200 OK2018-04-13
200 OK2018-04-10
200 OK2018-04-06
200 OK2018-04-03
200 OK2018-02-27
200 OK2018-02-23
200 OK2018-02-20
200 OK2018-02-16
200 OK2018-02-13
200 OK2018-02-09
200 OK2018-02-06
200 OK2018-02-02
200 OK2018-01-30
200 OK2018-01-26
200 OK2018-01-23
200 OK2018-01-19
200 OK2018-01-16
200 OK2018-01-12
200 OK2018-01-09
200 OK2018-01-05
200 OK2018-01-02
200 OK2017-12-29
200 OK2017-12-26
200 OK2017-12-22
200 OK2017-12-19
200 OK2017-12-15
200 OK2017-12-12
200 OK2017-12-08
200 OK2017-12-05
200 OK2017-12-01
200 OK2017-11-28
200 OK2017-11-24
200 OK2017-11-21
200 OK2017-11-17
200 OK2017-11-14
200 OK2017-11-10
200 OK2017-11-07
200 OK2017-11-03
200 OK2017-10-31
200 OK2017-10-27
200 OK2017-10-24
200 OK2017-10-20
200 OK2017-10-17
200 OK2017-10-13
200 OK2017-10-10
200 OK2017-10-06
200 OK2017-10-03
200 OK2017-09-29
200 OK2017-09-26
200 OK2017-09-22
200 OK2017-09-19
200 OK2017-09-15
200 OK2017-09-12
200 OK2017-09-08
200 OK2017-09-05
200 OK2017-09-01
200 OK2017-08-29
200 OK2017-08-25
200 OK2017-08-22
200 OK2017-08-18
200 OK2017-08-15
200 OK2017-08-11
200 OK2017-08-08
200 OK2017-08-04
200 OK2017-08-01
200 OK2017-07-28
200 OK2017-07-25
200 OK2017-07-21
200 OK2017-07-18
200 OK2017-07-14
200 OK2017-07-04
200 OK2017-06-30
200 OK2017-06-27
200 OK2017-06-23
200 OK2017-06-20
200 OK2017-06-16
200 OK2017-06-13
200 OK2017-06-09
200 OK2017-06-06
200 OK2017-06-02
200 OK2017-05-30
200 OK2017-05-26
200 OK2017-05-23
200 OK2017-05-19
200 OK2017-05-16
200 OK2017-05-12
200 OK2017-05-09
200 OK2017-05-05
200 OK2017-05-02
200 OK2017-04-28
200 OK2017-04-25
200 OK2017-04-21
200 OK2017-04-18
200 OK2017-04-14
200 OK2017-04-11
200 OK2017-04-07
200 OK2017-04-04
200 OK2017-03-31
200 OK2017-03-28
200 OK2017-03-24
200 OK2017-03-21
200 OK2017-03-17
200 OK2017-03-14
200 OK2017-03-10
200 OK2017-03-07
200 OK2017-03-03
200 OK2017-02-28
200 OK2017-02-24
200 OK2017-02-21
200 OK2017-02-17
200 OK2017-02-14
200 OK2017-02-10
200 OK2017-02-07
200 OK2017-02-03
200 OK2017-01-31
200 OK2017-01-27
200 OK2017-01-24
200 OK2017-01-20
200 OK2017-01-17
200 OK2017-01-13
200 OK2017-01-10
200 OK2017-01-06
200 OK2017-01-03
-1 Failed2016-12-30
200 OK2016-12-27
200 OK2016-12-23
200 OK2016-12-20
200 OK2016-12-16
200 OK2016-12-13
200 OK2016-12-09
200 OK2016-12-06
200 OK2016-12-02
200 OK2016-11-29
200 OK2016-11-25
200 OK2016-11-22
200 OK2016-11-18
200 OK2016-11-15
200 OK2016-11-11
200 OK2016-11-08
200 OK2016-11-04
-1 Failed2016-11-01
-1 Failed2016-10-28
200 OK2016-10-25
200 OK2016-10-21
200 OK2016-10-18
200 OK2016-10-14
200 OK2016-10-11
200 OK2016-10-07
200 OK2016-10-04
200 OK2016-09-30
200 OK2016-09-27
200 OK2016-09-23
200 OK2016-09-20
200 OK2016-09-16
200 OK2016-09-13
200 OK2016-09-09
200 OK2016-09-06
200 OK2016-09-02
200 OK2016-08-30
200 OK2016-08-26
200 OK2016-08-23
200 OK2016-08-19
200 OK2016-08-16
200 OK2016-08-12
200 OK2016-08-09
200 OK2016-08-05
200 OK2016-08-02
200 OK2016-07-29
200 OK2016-07-26
200 OK2016-07-22
200 OK2016-07-19
200 OK2016-07-15
200 OK2016-07-12
200 OK2016-07-08
200 OK2016-07-05
200 OK2016-07-01
200 OK2016-06-28
200 OK2016-06-24
200 OK2016-06-21
200 OK2016-06-17
200 OK2016-06-14
200 OK2016-06-10
200 OK2016-06-07
200 OK2016-06-03
200 OK2016-05-31
200 OK2016-05-27
200 OK2016-05-24
200 OK2016-05-20
200 OK2016-05-17
200 OK2016-05-13
200 OK2016-05-10
200 OK2016-05-06
200 OK2016-05-03
200 OK2016-04-29
200 OK2016-04-26
200 OK2016-04-22
200 OK2016-04-19
200 OK2016-04-15
200 OK2016-04-12
200 OK2016-04-08
200 OK2016-04-05
200 OK2016-04-01
200 OK2016-03-29
200 OK2016-03-28
200 OK2016-03-25
200 OK2016-03-23
200 OK2016-03-21
200 OK2016-03-18
200 OK2016-03-16
200 OK2016-03-14
200 OK2016-03-11
200 OK2016-03-09
200 OK2016-03-07
200 OK2016-03-04
200 OK2016-03-02
200 OK2016-02-29
200 OK2016-02-26
200 OK2016-02-24
200 OK2016-02-22
200 OK2016-02-19
200 OK2016-02-17
200 OK2016-02-15
200 OK2016-02-14
200 OK2016-02-12
200 OK2016-02-10
200 OK2016-02-08
200 OK2016-02-07
200 OK2016-02-05
200 OK2016-02-03
200 OK2016-02-01
200 OK2016-01-31
200 OK2016-01-29
200 OK2016-01-27
200 OK2016-01-25
200 OK2016-01-24
200 OK2016-01-22
200 OK2016-01-20
200 OK2016-01-18
200 OK2016-01-17
200 OK2016-01-15
200 OK2016-01-13
200 OK2016-01-11
200 OK2016-01-10
200 OK2016-01-08
200 OK2016-01-06
200 OK2016-01-04

Tags

DNA
Archaea Bacteria
orthology

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Lin Liu [2016-03-28]
    • Li Yang [2015-06-26]
Stats