Objective: Detect the longest open reading frames (ORFs) of multiple sequences in a Q-fasta file and tabulate the ORF data along with other general information.

Open reading frame is an important piece of information about a mRNA sequence. From an ORF sequence, a predicted protein sequence can be derived and subsequently used for studying its functional domains. In general, for a full-length mRNA, the longest open reading frame is the region coding for its protein. The sequence before the first ATG of the longest ORF is called 5’ untranslated region (5’UTR), and the sequence after the stop in the same frame is called the 3’ untranslated region (3’UTR).

The Open Reading Frame Detection function in GeneLooper™ 2.0 is a high-throughput program. The program also allows users to analyze either full-length or partial mRNA sequences and gives a most informative and straightforward presentation of ORF data.

Features:

1. Fast: Detect thousands of sequences in a few minutes.
3. Versatile: detect both full-length and partial sequences by the complete ORF and incomplete ORF method respectively.
4. Instant data report: immediately tabulated data.
5. Informative: including many pieces of useful information such as Accession, GI, Size, ORF location and 5’ UTR.

A sample of working interface:



Samples of the data file obtained in an ORF detection process:



Detecting the ORFs of all availabe full-length mRNA sequences from human takes about an hour, while the returned data are extremly informative. From this type of tabulated data and by few calculation steps, one can answer some fundamental biological questions, such as the average size and the size-distributions of human transcripts, the average sizes of the coding regions and 5’ untranslated regions. The incomplete ORF detection method allows one to study the coding regions of partial cDNAs, for example, to screen those with relatively long incomplete ORF because they are more likely to be genuine transcripts coding for proteins. The resulting table can also be used as the general information of your gene collections.