Protocol detail

Transposable Elements Annotation and Analysis

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Transposable elements were identified using Repeat-Masker [6 ] and MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat) [27 ,28 (link)]. This database provides a hierarchical classification of plant transposable elements and other repeat types. Before use, the database was screened for non-TE related sequences and the following identifiers were removed: 'bsr1' (containing cytochrome P450 and hydrolase sequences), 'k_1' (containing proton-ATPase sequence), and 'magellan_cone' (containing myb transcription factor sequence).
Receiver operating characteristic (ROC) curves were compared by the method of [29 (link)], as implemented in the MedCalc^®statistical software package.

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Kurtz S., Narechania A., Stein J.C, & Ware D. (2008). A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. BMC Genomics, 9, 517.

Publication 2008

Atpase Cone Cytochrome p450 Hydrolase Mips Plant Proton Transcription factor Transposable elements

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Protocol cited in 16 other protocols

Variable analysis

independent variables

Not explicitly mentioned

dependent variables

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control variables

Transposable elements were identified using Repeat-Masker and MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat). This database provides a hierarchical classification of plant transposable elements and other repeat types.
Before use, the database was screened for non-TE related sequences and the following identifiers were removed: 'bsr1' (containing cytochrome P450 and hydrolase sequences), 'k_1' (containing proton-ATPase sequence), and 'magellan_cone' (containing myb transcription factor sequence).

positive controls

Not mentioned

negative controls

Not mentioned

Annotations

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