MASiVE: Mapping and Analysis of Sirevirus Elements in plant genome sequences.
We present MASiVE, an expertly built tool for the large-scale, yet sensitive and highly accurate, discovery, preliminary analysis and insertion age estimation of intact Sirevirus LTR-retrotransposons in plant genomic sequences. Validation was based on the recently available and annotated large maize chromosome one. Results show a considerable improvement in the annotation of Sireviruses, and support our approach as an important addition to the bioinformatics toolbox of plant biologists.


BACKGROUND
PERL source code and essential files are available online at http://bat.ina.certh.gr/tools/masive/. The freely available Vmatch, LTRharvest, Wise2, and MAFFT algorithms are required.
Darzentas
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Institute of Agrobiotechnology, Centre for Research and Technology Hellas, Thessaloniki 57001, Greece. ndarz@certh.gr
Bousios
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A
Apostolidou
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V
Tsaftaris
A S
AS
D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D018745:Genome, Plant; D016679:Genome, Viral; D018626:Retroelements / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software; D003313:Zea mays / Q000235:genetics
D018626:Retroelements