A pipeline of programs for collecting and analyzing group II intron retroelement sequences from GenBank.
Mob DNA
; 4(1): 28, 2013 Dec 20.
Article
em En
| MEDLINE
| ID: mdl-24359548
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.
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1
Coleções:
01-internacional
Base de dados:
MEDLINE
Idioma:
En
Revista:
Mob DNA
Ano de publicação:
2013
Tipo de documento:
Article