Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences.
Gene
; 448(2): 207-13, 2009 Dec 15.
Article
in En
| MEDLINE
| ID: mdl-19651192
ABSTRACT
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).
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Phylogeny
/
RNA-Directed DNA Polymerase
/
Classification
/
Retroelements
Type of study:
Evaluation_studies
/
Prognostic_studies
Language:
En
Journal:
Gene
Year:
2009
Document type:
Article
Affiliation country:
United States