Automated characterization of potentially active retroid agents in the human genome

Marcella A. McClure, Hugh S. Richardson, Rochelle A. Clinton, Crystal M. Hepp, Brad A. Crowther, Eric F. Donaldson

Research output: Contribution to journalArticlepeer-review

15 Scopus citations


Retroid agents are genomes that encode the reverse transcriptase (RT) and replicate by way of an RNA intermediate. Some retroid agents are implicated in disease via insertional mutagenesis, while others have been found to encode proteins essential to primate reproduction or provide regulatory sequences for host cell processes. The Genome Parsing Suite (GPS), a generic multistep automated process, was developed to characterize all RT-like sequences in the human genome database and to annotate the gene complement of the retroid agents that encode these sequences. In this report the GPS analyzes all significant WU-tBLASTn hits returned for 30 representative RT queries. A total of 128,779 unique RT signals were identified, and 7594 of these were retrieved by RTs not previously reported in the human genome. We have identified 9652 full-length long interspersed nuclear elements (LINEs). Only 159 LINEs are without stop codons or frameshifts.

Original languageEnglish (US)
Pages (from-to)512-523
Number of pages12
Issue number4
StatePublished - Apr 2005
Externally publishedYes


  • Endogenous retroviruses
  • Genome Parsing Suite software
  • Repetitive elements
  • Retroid
  • Retroposons
  • Retrotransposons

ASJC Scopus subject areas

  • Genetics


Dive into the research topics of 'Automated characterization of potentially active retroid agents in the human genome'. Together they form a unique fingerprint.

Cite this