In molecular genetics, an open reading frame is the part of a reading frame that contains
no stop codons.
The transcription termination pause site is located after the ORF, beyond the translation
stop codon, because if transcription were to cease before the stop codon, an incomplete
protein would be made during translation.
Normally, inserts which interrupt the reading frame of a subsequent region after the start
codon cause frameshift mutation of the sequence and dislocate the sequences for stop codons.
Significance One common use of open reading frames is as
one piece of evidence to assist in gene prediction.
Long ORFs are often used, along with other evidence, to initially identify candidate
protein coding regions in a DNA sequence.
The presence of an ORF does not necessarily mean that the region is ever translated.
For example in a randomly generated DNA sequence with an equal percentage of each nucleotide,
a stop-codon would be expected once every 21 codons.
A simple gene prediction algorithm for prokaryotes might look for a start codon followed by an
open reading frame that is long enough to encode a typical protein, where the codon
usage of that region matches the frequency characteristic for the given organism's coding
regions.
By itself even a long open reading frame is not conclusive evidence for the presence of
a gene.
Example If a portion of a genome has been sequenced,
ORFs can be located by examining each of the three possible reading frames on each strand.
Possible stop codons in DNA are "TGA", "TAA" and "TAG".
Six-frame translation Since DNA has two anti-parallel strands, an
additional three reading frames arise, giving a possible six frame translations.
ORF finding tools ORF Finder: The ORF Finder is a graphical
analysis tool which finds all open reading frames of a selectable minimum size in a user's
sequence or in a sequence already in the database.
This tool identifies all open reading frames using the standard or alternative genetic
codes.
The deduced amino acid sequence can be saved in various formats and searched against the
sequence database using the WWW BLAST server.
The ORF Finder should be helpful in preparing complete and accurate sequence submissions.
It is also packaged with the Sequin sequence submission software.(sequence analyser)
ORF Investigator: ORF Investigator is a program which not only gives information about the
coding and non coding sequences but also can perform pairwise global alignment of different
gene/DNA regions sequences.
The tool efficiently finds the ORFs for corresponding amino acid sequences and converts them into
their single letter amino acid code, and provides their locations in the sequence.
The pairwise global alignment between the sequences makes it convenient to detect the
different mutations, including single nucleotide polymorphism.
Needleman and Wunsch algorithms are used for the gene alignment.
The ORF Investigator is written in the portable Perl programming language, and is therefore
available to users of all common operating systems.
ORFPredictor: OrfPredictor is a web server designed for identifying protein-coding regions
in expressed sequence tag-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.
See also Reading frame
Sequerome - A sequence profiling tool that links each BLAST record to the NCBI ORF enabling
complete ORF analysis of a BLAST report.
Putative gene References
External links ORF Investigator ORF finding and Gene alignment
program developed by Vivek Dhar Dwivedi and Sarad Kumar Mishra.
Translation and Open Reading Frames NCBI ORF finder - A web based interactive
tool for predicting and analysing ORFs from nucleotide sequences.
ORF finder - A web based interactive tool for predicting and analysing ORFs from nucleotide
sequences - hosted at bioinformatics.org hORFeome V5.1 - A web based interactive tool
for CCSB Human ORFeome Collection ORF Marker - A free, fast and multi-platform
desktop GUI tool for predicting and analyzing ORFs
StarORF - A multi-platform, java based, GUI tool for predicting and analyzing ORFs and
obtaining reverse complement sequence ORFPredictor - A webserver designed for ORF
prediction and translation of a batch of EST or cDNA sequences