08-17-2017, 12:39 AM
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Theory:
The ORF Finder (Open Reading Frame 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 WW 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.
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.
If a portion of a genome has been sequenced (e.g. 5'-ATCTAATGGTGCC-3'), ORFs can be located by examining each of the three possible reading frames on each strand. In this sequence two out of three possible reading frames are entirely open, meaning that they do not contain a stop codon:
..A TCT AA ATG GGT GCC..
..AT CTA AA TGG GTG CC..
..ATC TAA AAT GG TGC C..
Possible stop codons in DNA are "TGA", "TAA" and "TAG". Thus, the last reading frame in this example contains a stop codon (TAA), unlike the first two.
Procedure:
Retrieve the query nucleotide sequence in Fasta format from NCBI
(ncbi.nlm.nih.gov).
Log in to http://ncbi.nlm.nih.gov/gorf/gorf.html
Paste the respective sequence in the given input box.
Click the ORF find button
As soon as the run button is clicked the process continues for predicting the ORFs.
Open Reading Frames were obtained after complete execution of the program