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Bioinformatics. 2010 Oct 1;26(19):2452-4. doi: 10.1093/bioinformatics/btq454. Epub 2010 Aug 9.

MASiVE: Mapping and Analysis of Sirevirus Elements in plant genome sequences.

Author information

1
Institute of Agrobiotechnology, Centre for Research and Technology Hellas, Thessaloniki 57001, Greece. ndarz@certh.gr

Abstract

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.

PMID:
20696734
DOI:
10.1093/bioinformatics/btq454
[Indexed for MEDLINE]

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