Automated paleontology of repetitive DNA with REANNOTATE

doi:10.1186/1471-2164-9-614

BMC Genomics

Volume 9

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Automated paleontology of repetitive DNA with REANNOTATE

Vini Pereira¹^,2

¹Department of Life Sciences, Imperial College London, Silwood Park campus, Ascot, Berkshire SL5 7PY, UK

²Theoretical Systems Biology, Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK

author email corresponding author email

BMC Genomics 2008, 9:614doi:10.1186/1471-2164-9-614


Published:	18 December 2008

Additional files

Additional file 1:

Equivalence table of different reference sequences corresponding to the same families of ERVs. Names of reference LTRs and internal regions of primate ERVs in REPBASE UPDATE that correspond to the same ERV family may be dissimilar. This text file contains lists (one per line) of equivalent (i.e. assigned to the same ERV family) names. This file must be input to REANNOTATE for defragmentation of primate ERVs if the input annotation was performed with the REPBASE UPDATE library. The first name in each line is used by REANNOTATE to assign a family to an element model that may contain hits matching different reference sequences within an equivalence class.

Format: TXT Size: 4KB Download file

Additional file 2:

Script for pre-processing primate ERV names in REPEATMASKER annotation. A shell script for pre-processing REPEATMASKER annotation so that appropriate suffixes are added to the names of reference primate ERV internal regions (and LTRs). This is necessary for defragmentation of primate ERVs if the input annotation was performed with the REPBASE UPDATE library.

Format: SH Size: 1KB Download file

Additional file 3:

Output re-annotation of dispersed repeats in the maize accession [GENBANK: AF123535.1]. This is the main repeat re-annotation file output by REANNOTATE as a tab delimited text file. Each line corresponds to a repetitive element model.

Format: TXT Size: 16KB Download file

Additional file 4:

Description of data fields in the main re-annotation file. Data fields in Additional file 1.

Format: PDF Size: 49KB Download file

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Additional file 5:

REANNOTATE. Current version of REANNOTATE.

Format: PL Size: 251KB Download file

Additional file 6:

REANNOTATE user manual. User manual.

Format: PDF Size: 155KB Download file

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