Literature DB >> 20696734

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

N Darzentas1, A Bousios, V Apostolidou, A S Tsaftaris.   

Abstract

UNLABELLED: 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.

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Year:  2010        PMID： 20696734     DOI： 10.1093/bioinformatics/btq454

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  9 in total

1.  Finding and Characterizing Repeats in Plant Genomes.

Authors:  Jacques Nicolas; Sébastien Tempel; Anna-Sophie Fiston-Lavier; Emira Cherif
Journal:  Methods Mol Biol       Date:  2022

2.  MASiVEdb: the Sirevirus Plant Retrotransposon Database.

Authors:  Alexandros Bousios; Evangelia Minga; Nikoleta Kalitsou; Maria Pantermali; Aphrodite Tsaballa; Nikos Darzentas
Journal:  BMC Genomics       Date:  2012-04-30       Impact factor: 3.969

3.  The study of a barley epigenetic regulator, HvDME, in seed development and under drought.

Authors:  Aliki Kapazoglou; Vicky Drosou; Anagnostis Argiriou; Athanasios S Tsaftaris
Journal:  BMC Plant Biol       Date:  2013-10-31       Impact factor: 4.215

4.  A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response.

Authors:  Alexandros Bousios; Concepcion M Diez; Shohei Takuno; Vojtech Bystry; Nikos Darzentas; Brandon S Gaut
Journal:  Genome Res       Date:  2015-12-02       Impact factor: 9.043

5.  Considerations and complications of mapping small RNA high-throughput data to transposable elements.

Authors:  Alexandros Bousios; Brandon S Gaut; Nikos Darzentas
Journal:  Mob DNA       Date:  2017-02-15

6.  Patterns of selection in the evolution of a transposable element.

Authors:  Julie Dazenière; Alexandros Bousios; Adam Eyre-Walker
Journal:  G3 (Bethesda)       Date:  2022-05-06       Impact factor: 3.542

7.  A sensitive repeat identification framework based on short and long reads.

Authors:  Xingyu Liao; Min Li; Kang Hu; Fang-Xiang Wu; Xin Gao; Jianxin Wang
Journal:  Nucleic Acids Res       Date:  2021-09-27       Impact factor: 16.971

8.  The study of two barley type I-like MADS-box genes as potential targets of epigenetic regulation during seed development.

Authors:  Aliki Kapazoglou; Cawas Engineer; Vicky Drosou; Chrysanthi Kalloniati; Eleni Tani; Aphrodite Tsaballa; Evangelia D Kouri; Ioannis Ganopoulos; Emmanouil Flemetakis; Athanasios S Tsaftaris
Journal:  BMC Plant Biol       Date:  2012-09-17       Impact factor: 4.215

9.  Sirevirus LTR retrotransposons: phylogenetic misconceptions in the plant world.

Authors:  Alexandros Bousios; Nikos Darzentas
Journal:  Mob DNA       Date:  2013-03-04
  9 in total

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