title: 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 BLAST search of GenBank using a set of representative group II IEPs as queries. Subsequent steps download the corresponding genomic sequences and flanks, filter out non-group II introns, assign introns to phylogenetic subclasses, filter out incomplete and/or non-functional introns, and assign IEP sequences and RNA boundaries to the full-length introns. In the final step, the redundancy in the data set is reduced by grouping introns into sets of ≥95% identity, with one example sequence chosen to be the representative.
  
  
  CONCLUSIONS
  These programs should be useful for comprehensive identification of group II introns in sequence databases as data continue to rapidly accumulate.
authors.affiliation: Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1 N4, Canada.
authors.forename: Michael
authors.initials: M
authors.lastname: Abebe
authors.affiliation: Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1 N4, Canada.
authors.forename: Manuel A
authors.initials: MA
authors.lastname: Candales
authors.affiliation: Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1 N4, Canada.
authors.forename: Adrian
authors.initials: A
authors.lastname: Duong
authors.affiliation: Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1 N4, Canada.
authors.forename: Keyar S
authors.initials: KS
authors.lastname: Hood
authors.affiliation: Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1 N4, Canada.
authors.forename: Tony
authors.initials: T
authors.lastname: Li
authors.affiliation: Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1 N4, Canada.
authors.forename: Ryan A E
authors.initials: RAE
authors.lastname: Neufeld
authors.affiliation: Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1 N4, Canada.
authors.forename: Abat
authors.initials: A
authors.lastname: Shakenov
authors.affiliation: Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1 N4, Canada.
authors.forename: Runda
authors.initials: R
authors.lastname: Sun
authors.affiliation: Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1 N4, Canada.
authors.forename: Li
authors.initials: L
authors.lastname: Wu
authors.affiliation: Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1 N4, Canada.
authors.forename: Ashley M
authors.initials: AM
authors.lastname: Jarding
authors.affiliation: Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1 N4, Canada.
authors.forename: Cameron
authors.initials: C
authors.lastname: Semper
authors.affiliation: Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1 N4, Canada.
authors.forename: Steven
authors.initials: S
authors.lastname: Zimmerly