ParTIES: a toolbox for Paramecium interspersed DNA elimination studies

Bioinformatics. 2016 Feb 15;32(4):599-601. doi: 10.1093/bioinformatics/btv691. Epub 2015 Nov 20.

Abstract

Motivation: Developmental DNA elimination occurs in a wide variety of multicellular organisms, but ciliates are the only single-celled eukaryotes in which this phenomenon has been reported. Despite considerable interest in ciliates as models for DNA elimination, no standard methods for identification and characterization of the eliminated sequences are currently available.

Results: We present the Paramecium Toolbox for Interspersed DNA Elimination Studies (ParTIES), designed for Paramecium species, that (i) identifies eliminated sequences, (ii) measures their presence in a sequencing sample and (iii) detects rare elimination polymorphisms.

Availability and implementation: ParTIES is multi-threaded Perl software available at https://github.com/oarnaiz/ParTIES. ParTIES is distributed under the GNU General Public Licence v3.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Ciliophora Infections / genetics*
  • DNA, Protozoan / metabolism*
  • Genome, Protozoan
  • Interspersed Repetitive Sequences / genetics*
  • Paramecium / genetics*
  • Paramecium / isolation & purification
  • Protozoan Proteins / metabolism*
  • Software*

Substances

  • DNA, Protozoan
  • Protozoan Proteins