Database Commons a catalog of biological databases

Database Commons - Hoppsigen

Hoppsigen

Citations: 44

z-index 0.34

Short name Hoppsigen
Full name Homologous Processed Pseudogenes database
Description Hoppsigen is a nucleic database of homologous processed pseudogenes.
URL http://pbil.univ-lyon1.fr
Year founded 2005
Last update & version 2014-01-01    v4.0
Availability Free to all users
University/Institution hosted Université Claude Bernard–Lyon 1
Address 69622 Villeurbanne Cedex, France
City Villeurbanne Cedex
Province/State
Country/Region France
Contact name Adel Khelifi
Contact email khelifi@biomserv.univ-lyon1.fr
Data type(s)
Major organism(s)
Keyword(s)
  • human retroelement
  • mouse retroelement
  • processed pseudogene
Publication(s)
  • HOPPSIGEN: a database of human and mouse processed pseudogenes. [PMID: 15608268]

    Adel Khelifi, Khelifi Adel, Laurent Duret, Duret Laurent, Dominique Mouchiroud, Mouchiroud Dominique
    Nucleic acids research 2005:33(Database issue)
    44 Citations (Google Scholar as of 2016-01-18)

    Abstract: Processed pseudogenes result from reverse transcribed mRNAs. In general, because processed pseudogenes lack promoters, they are no longer functional from the moment they are inserted into the genome. Subsequently, they freely accumulate substitutions, insertions and deletions. Moreover, the ancestral structure of processed pseudogenes could be easily inferred using the sequence of their functional homologous genes. Owing to these characteristics, processed pseudogenes represent good neutral markers for studying genome evolution. Recently, there is an increasing interest for these markers, particularly to help gene prediction in the field of genome annotation, functional genomics and genome evolution analysis (patterns of substitution). For these reasons, we have developed a method to annotate processed pseudogenes in complete genomes. To make them useful to different fields of research, we stored them in a nucleic acid database after having annotated them. In this work, we screened both mouse and human complete genomes from ENSEMBL to find processed pseudogenes generated from functional genes with introns. We used a conservative method to detect processed pseudogenes in order to minimize the rate of false positive sequences. Within processed pseudogenes, some are still having a conserved open reading frame and some have overlapping gene locations. We designated as retroelements all reverse transcribed sequences and more strictly, we designated as processed pseudogenes, all retroelements not falling in the two former categories (having a conserved open reading or overlapping gene locations). We annotated 5823 retroelements (5206 processed pseudogenes) in the human genome and 3934 (3428 processed pseudogenes) in the mouse genome. Compared to previous estimations, the total number of processed pseudogenes was underestimated but the aim of this procedure was to generate a high-quality dataset. To facilitate the use of processed pseudogenes in studying genome structure and evolution, DNA sequences from processed pseudogenes, and their functional reverse transcribed homologs, are now stored in a nucleic acid database, HOPPSIGEN. HOPPSIGEN can be browsed on the PBIL (Pole Bioinformatique Lyonnais) World Wide Web server (http://pbil.univ-lyon1.fr/) or fully downloaded for local installation.

Community reviews

Data
quality & quantity
Content organization & presentation
System accessibility & reliability
Reviewed by

Word cloud (embeddable)

Database Commons - Word Cloud

Accessibility

Rate of accessibility:
HTTP status codeDate requested
403 Failed2018-11-13
403 Failed2018-11-09
403 Failed2018-11-06
403 Failed2018-11-02
403 Failed2018-10-30
403 Failed2018-10-26
403 Failed2018-10-23
403 Failed2018-10-19
403 Failed2018-10-16
403 Failed2018-10-12
403 Failed2018-10-09
403 Failed2018-10-05
403 Failed2018-10-02
403 Failed2018-09-28
403 Failed2018-09-25
403 Failed2018-09-21
403 Failed2018-09-18
403 Failed2018-09-14
403 Failed2018-09-11
403 Failed2018-09-07
403 Failed2018-09-04
403 Failed2018-08-31
403 Failed2018-08-28
403 Failed2018-08-24
403 Failed2018-08-21
403 Failed2018-08-17
403 Failed2018-08-14
403 Failed2018-08-10
403 Failed2018-08-07
403 Failed2018-08-03
403 Failed2018-07-31
403 Failed2018-07-27
403 Failed2018-07-24
403 Failed2018-07-20
403 Failed2018-07-17
403 Failed2018-07-13
403 Failed2018-07-10
403 Failed2018-07-06
403 Failed2018-07-03
403 Failed2018-06-29
403 Failed2018-06-26
403 Failed2018-06-22
403 Failed2018-06-19
403 Failed2018-06-15
403 Failed2018-06-12
403 Failed2018-06-08
403 Failed2018-06-05
403 Failed2018-06-01
403 Failed2018-05-29
403 Failed2018-05-25
403 Failed2018-05-22
403 Failed2018-05-18
403 Failed2018-05-15
403 Failed2018-05-11
403 Failed2018-05-08
403 Failed2018-05-04
403 Failed2018-05-01
403 Failed2018-04-27
403 Failed2018-04-24
403 Failed2018-04-20
403 Failed2018-04-17
403 Failed2018-04-13
403 Failed2018-04-10
403 Failed2018-04-06
403 Failed2018-04-03
403 Failed2018-02-27
403 Failed2018-02-23
403 Failed2018-02-20
403 Failed2018-02-16
403 Failed2018-02-13
403 Failed2018-02-09
403 Failed2018-02-06
403 Failed2018-02-02
403 Failed2018-01-30
403 Failed2018-01-26
403 Failed2018-01-23
403 Failed2018-01-19
-1 Failed2018-01-16
403 Failed2018-01-12
403 Failed2018-01-09
403 Failed2018-01-05
403 Failed2018-01-02
403 Failed2017-12-29
403 Failed2017-12-26
403 Failed2017-12-22
403 Failed2017-12-19
403 Failed2017-12-15
403 Failed2017-12-12
403 Failed2017-12-08
403 Failed2017-12-05
403 Failed2017-12-01
403 Failed2017-11-28
403 Failed2017-11-24
403 Failed2017-11-21
403 Failed2017-11-17
403 Failed2017-11-14
403 Failed2017-11-10
403 Failed2017-11-07
403 Failed2017-11-03
403 Failed2017-10-31
403 Failed2017-10-27
403 Failed2017-10-24
403 Failed2017-10-20
403 Failed2017-10-17
-1 Failed2017-10-13
403 Failed2017-10-10
403 Failed2017-10-06
403 Failed2017-10-03
403 Failed2017-09-29
403 Failed2017-09-26
403 Failed2017-09-22
403 Failed2017-09-19
403 Failed2017-09-15
403 Failed2017-09-12
403 Failed2017-09-08
403 Failed2017-09-05
403 Failed2017-09-01
403 Failed2017-08-29
403 Failed2017-08-25
403 Failed2017-08-22
403 Failed2017-08-18
403 Failed2017-08-15
403 Failed2017-08-11
403 Failed2017-08-08
403 Failed2017-08-04
403 Failed2017-08-01
403 Failed2017-07-28
403 Failed2017-07-25
403 Failed2017-07-21
403 Failed2017-07-18
403 Failed2017-07-14
403 Failed2017-07-04
403 Failed2017-06-30
403 Failed2017-06-27
403 Failed2017-06-23
403 Failed2017-06-20
403 Failed2017-06-16
403 Failed2017-06-13
403 Failed2017-06-09
403 Failed2017-06-06
403 Failed2017-06-02
403 Failed2017-05-30
403 Failed2017-05-26
403 Failed2017-05-23
403 Failed2017-05-19
403 Failed2017-05-16
403 Failed2017-05-12
403 Failed2017-05-09
403 Failed2017-05-05
403 Failed2017-05-02
403 Failed2017-04-28
403 Failed2017-04-25
403 Failed2017-04-21
403 Failed2017-04-18
403 Failed2017-04-14
403 Failed2017-04-11
403 Failed2017-04-07
403 Failed2017-04-04
403 Failed2017-03-31
403 Failed2017-03-28
403 Failed2017-03-24
403 Failed2017-03-21
403 Failed2017-03-17
403 Failed2017-03-14
403 Failed2017-03-10
403 Failed2017-03-07
403 Failed2017-03-03
403 Failed2017-02-28
403 Failed2017-02-24
403 Failed2017-02-21
403 Failed2017-02-17
403 Failed2017-02-14
403 Failed2017-02-10
403 Failed2017-02-07
403 Failed2017-02-03
403 Failed2017-01-31
403 Failed2017-01-27
403 Failed2017-01-24
403 Failed2017-01-20
403 Failed2017-01-17
403 Failed2017-01-13
403 Failed2017-01-10
403 Failed2017-01-06
403 Failed2017-01-03
403 Failed2016-12-30
403 Failed2016-12-27
403 Failed2016-12-23
403 Failed2016-12-20
403 Failed2016-12-16
403 Failed2016-12-13
403 Failed2016-12-09
403 Failed2016-12-06
403 Failed2016-12-02
403 Failed2016-11-29
403 Failed2016-11-25
403 Failed2016-11-22
403 Failed2016-11-18
403 Failed2016-11-15
403 Failed2016-11-11
403 Failed2016-11-08
403 Failed2016-11-04
403 Failed2016-11-01
403 Failed2016-10-28
403 Failed2016-10-25
403 Failed2016-10-21
403 Failed2016-10-18
403 Failed2016-10-14
403 Failed2016-10-11
403 Failed2016-10-07
403 Failed2016-10-04
403 Failed2016-09-30
403 Failed2016-09-27
403 Failed2016-09-23
403 Failed2016-09-20
403 Failed2016-09-16
403 Failed2016-09-13
403 Failed2016-09-09
403 Failed2016-09-06
403 Failed2016-09-02
403 Failed2016-08-30
403 Failed2016-08-26
403 Failed2016-08-23
403 Failed2016-08-19
403 Failed2016-08-16
403 Failed2016-08-12
403 Failed2016-08-09
403 Failed2016-08-05
403 Failed2016-08-02
403 Failed2016-07-29
403 Failed2016-07-26
403 Failed2016-07-22
403 Failed2016-07-19
403 Failed2016-07-15
403 Failed2016-07-12
403 Failed2016-07-08
403 Failed2016-07-05
403 Failed2016-07-01
403 Failed2016-06-28
403 Failed2016-06-24
403 Failed2016-06-21
403 Failed2016-06-17
403 Failed2016-06-14
403 Failed2016-06-10
403 Failed2016-06-07
403 Failed2016-06-03
403 Failed2016-05-31
403 Failed2016-05-27
403 Failed2016-05-24
403 Failed2016-05-20
403 Failed2016-05-17
403 Failed2016-05-13
403 Failed2016-05-10
403 Failed2016-05-06
403 Failed2016-05-03
403 Failed2016-04-29
403 Failed2016-04-26
403 Failed2016-04-22
403 Failed2016-04-19
403 Failed2016-04-15
403 Failed2016-04-12
403 Failed2016-04-08
403 Failed2016-04-05
403 Failed2016-04-01
403 Failed2016-03-29
403 Failed2016-03-28
403 Failed2016-03-25
403 Failed2016-03-23
403 Failed2016-03-21
403 Failed2016-03-18
403 Failed2016-03-16
403 Failed2016-03-14
403 Failed2016-03-11
403 Failed2016-03-09
403 Failed2016-03-07
403 Failed2016-03-04
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
Homo sapiens Mus musculus
human retroelement mouse retroelement processed pseudogene

Record metadata

  • Created on: 2015-07-10
  • Curated by:
    • Chunlei Yu [2016-04-17]
    • Lina Ma [2016-04-08]
    • Chunlei Yu [2016-03-31]
    • Mengwei Li [2016-02-20]
    • Zhang Zhang [2016-01-06]
    • Chunlei Yu [2015-11-19]
    • Chunlei Yu [2015-07-10]
Stats