Editing Open reading frame (section)

===Predictor===
OrfPredictor<ref>{{cite web|url=http://bioinformatics.ysu.edu/tools/OrfPredictor.html|title=OrfPredictor|website=bioinformatics.ysu.edu|access-date=2015-12-17|archive-date=2015-12-22|archive-url=https://web.archive.org/web/20151222082631/http://bioinformatics.ysu.edu/tools/OrfPredictor.html|url-status=dead}}</ref> is a web server designed for identifying protein-coding regions in expressed sequence tag (EST)-derived sequences. For query sequences with a hit in BLASTX, the program predicts the coding regions based on the translation reading frames identified in BLASTX alignments, otherwise, it predicts the most probable coding region based on the intrinsic signals of the query sequences. The output is the predicted peptide sequences in the [[FASTA format]], and a definition line that includes the query ID, the translation reading frame and the nucleotide positions where the coding region begins and ends. OrfPredictor facilitates the annotation of EST-derived sequences, particularly, for large-scale EST projects.

ORF Predictor uses a combination of the two different ORF definitions mentioned above. It searches stretches starting with a start codon and ending at a stop codon. As an additional criterion, it searches for a stop codon in the 5' [[untranslated region]] (UTR or NTR, ''nontranslated region''<ref name="Carrington_1990">{{cite journal | vauthors = Carrington JC, Freed DD | title = Cap-independent enhancement of translation by a plant potyvirus 5' nontranslated region | journal = Journal of Virology | volume = 64 | issue = 4 | pages = 1590–7 | date = April 1990 | pmid = 2319646 | pmc = 249294 | doi = 10.1128/JVI.64.4.1590-1597.1990 }}</ref>). The OrfPredictor web server was not further supported, the standalone OrfPredictor tool can be downloaded at the following site (http://bioinformatics.ysu.edu/publication/tools_download/).