View source for Repeat Library Construction - Basic

''Content contributed by [http://www.hrt.msu.edu/ning-jiang/ Dr. Ning Jiang]''

Building custom repeat library for plant genomes – Basic protocol

== 1.	Collecting repetitive sequences by [http://www.repeatmasker.org/RepeatModeler.html RepeatModeler] ==

The genomic sequence  (called seqfile) was processed by RepeatModeler

First command:
 DIR/BuildDatabase -name umseqfiledb -engine ncbi seqfile
*DIR = path where RepeatModeler is.
*“-engine ncbi” refers to that NCBI blast program was used as alignment tool. 

Second command:
 nohup DIR/RepeatModeler -database seqfiledb >& seqfile.out
*Among the sequences generated by RepeatModeler, some were associated with identities and others were not. These with identities were put in ModelerID.lib and the others were in Modelerunknown.lib.
*Sequences in Modelerunknown.lib were searched against a transposase database (derived from [http://www.repeatmasker.org/ RepeatMasker] package and [http://www.ncbi.nlm.nih.gov/pubmed/21535899 Kennedy et al (2011)]) and sequences matching transposase were considered as transposons belonging to the relevant superfamily and were incorporated into ModelerID.lib and excluded from Modelerunknown.lib. 

== 2.	Exclusion of gene fragments ==

*All repeats collected by RepeatModeler were used to search against a plant protein database where proteins from transposons were excluded. Sequences match the plants proteins as well as 50 bp flanking sequences were excluded. After the exclusion if the remainder sequences were shorter than 50 bp, the entire sequence was excluded. A package for conducting this task is available [here].
*After exclusion of putative gene fragments, ModelerID.lib were considered as know TE sequences (AtBasicTE.lib)
*AtBasicTE.lib was combined with Modelerunknown.lib (after exclusion of gene fragments) to form AtBasicAllRepeat.lib.
*It is conceivable that AtBasicTE.lib does not contain all repeats (repeats numbers are underestimated); AtBasicAllRepeat.lib may contain sequences from novel gene families (Repeat number are overestimated).