A pipeline of programs for collecting and analyzing group II intron retroelement sequences from GenBank.

ABSTRACT:

Background

Accurate and complete identification of mobile elements is a challenging task in the current era of sequencing, given their large numbers and frequent truncations. Group II intron retroelements, which consist of a ribozyme and an intron-encoded protein (IEP), are usually identified in bacterial genomes through their IEP; however, the RNA component that defines the intron boundaries is often difficult to identify because of a lack of strong sequence conservation corresponding to the RNA structure. Compounding the problem of boundary definition is the fact that a majority of group II intron copies in bacteria are truncated.

Results

Here we present a pipeline of 11 programs that collect and analyze group II intron sequences from GenBank. The pipeline begins with a BL

SUBMITTER: Abebe M 

PROVIDER: S-EPMC4028801 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature