title: Automated characterization of potentially active retroid agents in the human genome.
abstract: 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.
authors.affiliation: Department of Microbiology and the Center for Computational Biology, Montana State University at Bozeman, 109 Lewis Hall, Bozeman, MT 59717, USA. mars@parvati.msu.montana.edu
authors.forename: Marcella A
authors.initials: MA
authors.lastname: McClure
authors.forename: Hugh S
authors.initials: HS
authors.lastname: Richardson
authors.forename: Rochelle A
authors.initials: RA
authors.lastname: Clinton
authors.forename: Crystal M
authors.initials: CM
authors.lastname: Hepp
authors.forename: Brad A
authors.initials: BA
authors.lastname: Crowther
authors.forename: Eric F
authors.initials: EF
authors.lastname: Donaldson
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D020077:Endogenous Retroviruses / Q000235:genetics*; D015894:Genome, Human; D006801:Humans; D020084:Long Interspersed Nucleotide Elements; D008969:Molecular Sequence Data; D012194:RNA-Directed DNA Polymerase / Q000235:genetics*; D018626:Retroelements / Q000235:genetics*; D012984:Software
chemical_list: D018626:Retroelements; D012194:RNA-Directed DNA Polymerase