Approach Schematic. The approach is composed of multiple, iterative steps. The general flow is as follows. A TE family is used in a BLAST search against the genome. Hits are then combined, extracted from the genome, and assembled with CAP3. Next, the sequences are trimmed and again used in a BLAST search against the genome. The results are then used to produce a multiple sequence alignment in ClustalW2. We generate a consensus from the alignment, and then perform a final BLAST search against the genome. We again combine, extract, and assemble with CAP3. Lastly, the consensus TE is generated from CAP3.
Kennedy et al. BMC Bioinformatics 2011 12:130 doi:10.1186/1471-2105-12-130