We note that our method is a de novo method that does not rely on a library of known elements.
In this paper, we report a de novo computational method that can identify new LTR retrotransposons without relying on a library of known elements.
Interspersed repeats and low complexity regions in all clusters were masked by screening against a library of repetitive elements if available for the organism by RepeatMasker [ 34].
When we used RepeatMasker to annotate retroelements in C. briggsae based on a library of LTR elements in C. elegans, we got 74 hits, but most of them were short partial matching and no significant hit was found.
In addition, EST reads were screened against RepBase (version 13.06) [ 27], a library of repetitive elements, and returned as masked sequences ready for the clustering/assembling and annotation procedures.
Use of either a library of transposable element sequences constructed from the G. magnirostris genome (using RepeatScout [ 22]) or a zebra finch repeat library resulted in the identification of 3.3% or 4.1% of the assembly as being repetitive, respectively.
This model has been employed by the Dominguez group to screen for modifiers of this phenotype using a library of P-element UAS insertion lines that result in gene overexpression(Ferres-Marco et al., 2006).
Click comes with an extensive library of elements supporting various types of packet manipulations.
Helixhunter's results can in turn be used to probe a library of secondary structure elements derived from the structures in the Protein Data Bank (PDB).
As a 2000 profile in Cinefex recounts, Blue Sky Studios did CGI for the movie and since they were formerly associated with a company called VIFX that worked on "Titanic," Blue Sky had a "library of generic breath elements created for 'Titanic'" at their disposal.
