Document Detail


Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences.
MedLine Citation:
PMID:  19651192     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Rapidly growing number of sequenced genomes requires fast and accurate computational tools for analysis of different transposable elements (TEs). In this paper we focus on a rapid and reliable procedure for classification of autonomous non-LTR retrotransposons based on alignment and clustering of their reverse transcriptase (RT) domains. Typically, the RT domain protein sequences encoded by different non-LTR retrotransposons are similar to each other in terms of significant BLASTP E-values. Therefore, they can be easily detected by the routine BLASTP searches of genomic DNA sequences coding for proteins similar to the RT domains of known non-LTR retrotransposons. However, detailed classification of non-LTR retrotransposons, i.e. their assignment to specific clades, is a slow and complex procedure that is not formalized or integrated as a standard set of computational methods and data. Here we describe a tool (RTclass1) designed for the fast and accurate automated assignment of novel non-LTR retrotransposons to known or novel clades using phylogenetic analysis of the RT domain protein sequences. RTclass1 classifies a particular non-LTR retrotransposon based on its RT domain in less than 10 min on a standard desktop computer and achieves 99.5% accuracy. RT1class1 works either as a stand-alone program installed locally or as a web-server that can be accessed distantly by uploading sequence data through the internet (http://www.girinst.org/RTphylogeny/RTclass1).
Authors:
Vladimir V Kapitonov; Sébastien Tempel; Jerzy Jurka
Publication Detail:
Type:  Evaluation Studies; Journal Article; Research Support, N.I.H., Extramural     Date:  2009-08-03
Journal Detail:
Title:  Gene     Volume:  448     ISSN:  1879-0038     ISO Abbreviation:  Gene     Publication Date:  2009 Dec 
Date Detail:
Created Date:  2009-10-30     Completed Date:  2009-12-02     Revised Date:  2013-06-02    
Medline Journal Info:
Nlm Unique ID:  7706761     Medline TA:  Gene     Country:  Netherlands    
Other Details:
Languages:  eng     Pagination:  207-13     Citation Subset:  IM    
Affiliation:
Genetic Information Research Institute, 1925 Landings Dr, Mountain View, CA 94041, USA. vladimir@girinst.org
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MeSH Terms
Descriptor/Qualifier:
Algorithms
Amino Acid Sequence
Classification / methods*
Models, Genetic
Phylogeny*
Protein Structure, Tertiary / genetics
RNA-Directed DNA Polymerase / chemistry,  genetics*
Reproducibility of Results
Retroelements* / genetics
Sequence Analysis, DNA / methods
Terminal Repeat Sequences / genetics
Grant Support
ID/Acronym/Agency:
5 P41 LM006252/LM/NLM NIH HHS; P41 LM006252-12/LM/NLM NIH HHS
Chemical
Reg. No./Substance:
0/Retroelements; EC 2.7.7.49/RNA-Directed DNA Polymerase
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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