miRAFinder and GeneAFinder scripts: large-scale searching for miRNA and related information in indexed literature abstracts

Olga Berillo; Mireille Régnier; Anatoly Ivashchenko

doi:10.6026/97320630010539

miRAFinder and GeneAFinder scripts: large-scale searching for miRNA and related information in indexed literature abstracts

Bioinformation. 2014 Aug 30;10(8):539-43. doi: 10.6026/97320630010539. eCollection 2014.

Authors

Olga Berillo¹, Mireille Régnier², Anatoly Ivashchenko¹

Affiliations

¹ National nanotechnology laboratory, al-Farabi Kazakh National University, Almaty, Kazakhstan.
² INRIA/LIX team AMIB, École Polytechnique, Palaiseau, France.

Abstract

In recent times, information on miRNAs and their binding sites is gaining momentum. Therefore, there is interest in the development of tools extracting miRNA related information from known literature. Hence, we describe GeneAFinder and miRAFinder scripts (open source) developed using python programming for the semi-automatic extraction and arrangement of updated information on miRNAs, genes and additional data from published article abstracts in PubMed. The scripts are suitable for custom modification as per requirement.

Availability: miRAFinder and GeneAFinder scripts are free and available for download at http://sites.google.com /site/malaheenee/software.

Keywords: gene information; miRNA information; python script; semi-automatic extraction.