Transposon Insertion Finder (TIF): a novel program for detection of de novo transpositions of transposable elements.

ABSTRACT:

Background

Transposition event detection of transposable element (TE) in the genome using short reads from the next-generation sequence (NGS) was difficult, because the nucleotide sequence of TE itself is repetitive, making it difficult to identify locations of its insertions by alignment programs for NGS. We have developed a program with a new algorithm to detect the transpositions from NGS data.

Results

In the process of tool development, we used next-generation sequence (NGS) data of derivative lines (ttm2 and ttm5) of japonica rice cv. Nipponbare, regenerated through cell culture. The new program, called a transposon insertion finder (TIF), was applied to detect the de novo transpositions of Tos17 in the regenerated lines. TIF searched 300 million reads of a line within

SUBMITTER: Nakagome M 

PROVIDER: S-EPMC4004357 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature