Literature DB >> 23233656

RetroSeq: transposable element discovery from next-generation sequencing data.

Thomas M Keane1, Kim Wong, David J Adams.   

Abstract

A significant proportion of eukaryote genomes consist of transposable element (TE)-derived sequence. These elements are known to have the capacity to modulate gene function and genome evolution. We have developed RetroSeq for detecting non-reference TE insertions from Illumina paired-end whole-genome sequencing data. We evaluate RetroSeq on a human trio from the 1000 Genomes Project, showing that it produces highly accurate TE calls. AVAILABILTY: RetroSeq is open-source and available from https://github.com/tk2/RetroSeq.

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Mesh：

Year:  2012        PMID： 23233656      PMCID： PMC3562067          DOI： 10.1093/bioinformatics/bts697

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


  15 in total

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5.  Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition.

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7.  Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery.

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8.  Retroviral elements and their hosts: insertional mutagenesis in the mouse germ line.

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9.  Automated generation of heuristics for biological sequence comparison.

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10.  Fast and accurate short read alignment with Burrows-Wheeler transform.

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Journal:  Bioinformatics       Date:  2009-05-18       Impact factor: 6.937
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  86 in total

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Journal:  Brief Bioinform       Date:  2017-11-01       Impact factor: 11.622

6.  The genomic landscape of polymorphic human nuclear mitochondrial insertions.

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7.  Whole-Genome Resequencing Reveals Extensive Natural Variation in the Model Green Alga Chlamydomonas reinhardtii.

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Review 8.  Transposable element detection from whole genome sequence data.

Authors:  Adam D Ewing
Journal:  Mob DNA       Date:  2015-12-29

9.  TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data.

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10.  The effect of hybridization on transposable element accumulation in an undomesticated fungal species.

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