LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons.

ABSTRACT:

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Background

Long terminal repeat (LTR) retrotransposons are a class of eukaryotic mobile elements characterized by a distinctive sequence similarity-based structure. Hence they are well suited for computational identification. Current software allows for a comprehensive genome-wide de novo detection of such elements. The obvious next step is the classification of newly detected candidates resulting in (super-)families. Such a de novo classification approach based on sequence-based clustering of transposon features has been proposed before, resulting in a preliminary assignment of candidates to families as a basis for subsequent manual refinement. However, such a classification workflow is typically split across a heterogeneous set of glue scripts and generic softw

SUBMITTER: Steinbiss S 

PROVIDER: S-EPMC3582472 | biostudies-literature | 2012 Nov

REPOSITORIES: biostudies-literature