ORF Miner: a Web-based ORF Search Tool.

Park,  Sin Gi; Kim,  Ki Bong

doi:2009.7.4.217

Genomics Inform > Volume 7(4); 2009 > Article

Note

Genomics & Informatics 2009;7(4): 217-219.

DOI: https://doi.org/10.5808/gi.2009.7.4.217

ORF Miner: a Web-based ORF Search Tool.

Sin Gi Park, Ki Bong Kim

Department of Medical Biotechnology, Sangmyung University, Cheonan 330-720, Korea. kbkim@smu.ac.kr

Abstract

The primary clue for locating protein-coding regions is the open reading frame and the determination of ORFs (Open Reading Frames) is the first step toward the gene prediction, especially for prokaryotes. In this respect, we have developed a web-based ORF search tool called ORF Miner. The ORF Miner is a graphical analysis utility which determines all possible open reading frames of a selectable minimum size in an input sequence. This tool identifies all open reading frames using alternative genetic codes as well as the standard one and reports a list of ORFs with corresponding deduced amino acid sequences. The ORF Miner can be employed for sequence annotation and give a crucial clue to determination of actual protein-coding regions.

Keywords: alternative genetic codes; gene prediction; open reading frame; ORF Miner; protein-coding region