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...

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Veröffentlicht in:	Bioinformatics 2010-10, Vol.26 (19), p.2452-2454
Hauptverfasser:	Darzentas, N., Bousios, A., Apostolidou, V., Tsaftaris, A. S.
Format:	Artikel
Sprache:	eng
Schlagworte:	Base Sequence Biological and medical sciences Computational Biology - methods Databases, Genetic Fundamental and applied biological sciences. Psychology General aspects Genome, Plant Genome, Viral Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Retroelements - genetics Sequence Analysis, DNA - methods Software Zea mays Zea mays - genetics
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Beschreibung
Zusammenfassung:	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. Availability: 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. Contact: ndarz@certh.gr Supplementary information: Supplementary data are available at Bioinformatics online.
ISSN:	1367-4803 1460-2059 1367-4811
DOI:	10.1093/bioinformatics/btq454