gene/ORF - (Dec/03/2006 )
hi all,
i'm looking for detailed info about the differences between genes and orfs, orf prediction, what i found was just outlined or summarized info.. 
, share me your opinions..
my regards 
ok
try these sites in the following order and if u still dont get it i will be back
http://en.wikipedia.org/wiki/Gene
http://en.wikipedia.org/wiki/Open_reading_frame
http://bioweb.uwlax.edu/GenWeb/Molecular/S...ranslation.html
this is a pdf lecture about ORF /GENES
http://manatee.sourceforge.net/pdf/overview.pdf
To make it easier for u
first genes are a series of paired nucleotides at a particular location on a chromosome, these paired nucleotides contain the basic blueprint for a particular protein.
The part of the mRNA molecule that contains this information is known as its coding region, and it is composed of a series of clusters of three nucleotides known as codons. Each of the 64 different codons designates a specific amino acid except for three: TAA, TAG and TGA, which are known as stop codons. These three codons signal the ribosome to stop reading, ending the production of the protein.
this means that a given mRNA molecule can be read in three different ways, to create three different protein sequences. To illustrate:
..T CTC AGC GTT ACC ATG A..
... Leu Ser Val Thr Met ...
The first line is the mRNA sequence ), while the second line is the corresponding amino acid sequence . This is all well and good, but what happens if you start the decoding process one nucleotide later?
.TC TCA GCG TTA CCA TGA
... Ser Ala Leu Pro STOP!
Instead of coding for the functional protein sequence Leu-Ser-Val-Thr-Met-etc., the mRNA now codes for a completely different set of amino acids, including a TGA stop codon. Thus the information in the mRNA molecule is only useful if it is read in the correct way; otherwise the end result is protein gibberish, usually coming to an abrupt halt after a few dozen codons (since 3 of the 64 codons are stop codons, almost one in twenty random codons will halt translation).
Each of the three different ways of reading mRNA are known as reading frames. Any reading frame which does not contain a stop codon is known as an open reading frame. In practice, the longest open reading frame in an mRNA is generally the one that encodes the protein. For this reason, searching for open reading frames (or ORFs, as they are commonly known) is a simple way of finding genes in a newly sequenced piece of an organism's genome. Basically, if you find a long ORF, you've probably found a gene.
hope this help.
first genes are a series of paired nucleotides at a particular location on a chromosome, these paired nucleotides contain the basic blueprint for a particular protein.
The part of the mRNA molecule that contains this information is known as its coding region, and it is composed of a series of clusters of three nucleotides known as codons. Each of the 64 different codons designates a specific amino acid except for three: TAA, TAG and TGA, which are known as stop codons. These three codons signal the ribosome to stop reading, ending the production of the protein.
this means that a given mRNA molecule can be read in three different ways, to create three different protein sequences. To illustrate:
..T CTC AGC GTT ACC ATG A..
... Leu Ser Val Thr Met ...
The first line is the mRNA sequence ), while the second line is the corresponding amino acid sequence . This is all well and good, but what happens if you start the decoding process one nucleotide later?
.TC TCA GCG TTA CCA TGA
... Ser Ala Leu Pro STOP!
Instead of coding for the functional protein sequence Leu-Ser-Val-Thr-Met-etc., the mRNA now codes for a completely different set of amino acids, including a TGA stop codon. Thus the information in the mRNA molecule is only useful if it is read in the correct way; otherwise the end result is protein gibberish, usually coming to an abrupt halt after a few dozen codons (since 3 of the 64 codons are stop codons, almost one in twenty random codons will halt translation).
Each of the three different ways of reading mRNA are known as reading frames. Any reading frame which does not contain a stop codon is known as an open reading frame. In practice, the longest open reading frame in an mRNA is generally the one that encodes the protein. For this reason, searching for open reading frames (or ORFs, as they are commonly known) is a simple way of finding genes in a newly sequenced piece of an organism's genome. Basically, if you find a long ORF, you've probably found a gene.
hope this help.
So what'd b the so-called features of an ORF..?
an AUG at the beginning.. ?
hmm.. what else..
i mean.. given a sequence.. how wud u identify an ORF?
Thanks! thanx spanishflower ..i'll check the sites
hope this help.
yes it helps..
i already know the story of 6 reading frames, but what i just know now is why ORFs are called open..
...but eventually they will end with a stop codon ..right? 
what makes me soo confused is if you have a long DNA sequence and no web tool to find ORFs, what are you going to do? search for ATGs? also, it will be so hard to check for all 6 frames
first genes are a series of paired nucleotides at a particular location on a chromosome, these paired nucleotides contain the basic blueprint for a particular protein.
The part of the mRNA molecule that contains this information is known as its coding region, and it is composed of a series of clusters of three nucleotides known as codons. Each of the 64 different codons designates a specific amino acid except for three: TAA, TAG and TGA, which are known as stop codons. These three codons signal the ribosome to stop reading, ending the production of the protein.
this means that a given mRNA molecule can be read in three different ways, to create three different protein sequences. To illustrate:
..T CTC AGC GTT ACC ATG A..
... Leu Ser Val Thr Met ...
The first line is the mRNA sequence ), while the second line is the corresponding amino acid sequence . This is all well and good, but what happens if you start the decoding process one nucleotide later?
.TC TCA GCG TTA CCA TGA
... Ser Ala Leu Pro STOP!
Instead of coding for the functional protein sequence Leu-Ser-Val-Thr-Met-etc., the mRNA now codes for a completely different set of amino acids, including a TGA stop codon. Thus the information in the mRNA molecule is only useful if it is read in the correct way; otherwise the end result is protein gibberish, usually coming to an abrupt halt after a few dozen codons (since 3 of the 64 codons are stop codons, almost one in twenty random codons will halt translation).
Each of the three different ways of reading mRNA are known as reading frames. Any reading frame which does not contain a stop codon is known as an open reading frame. In practice, the longest open reading frame in an mRNA is generally the one that encodes the protein. For this reason, searching for open reading frames (or ORFs, as they are commonly known) is a simple way of finding genes in a newly sequenced piece of an organism's genome. Basically, if you find a long ORF, you've probably found a gene.
hope this help.
So what'd b the so-called features of an ORF..?
an AUG at the beginning.. ?
hmm.. what else..
i mean.. given a sequence.. how wud u identify an ORF?
Thanks!hi there
The codon AUG(methionine) is the "Start" message for a ribosome to begin ANY protein translation from mRNA. As a consequence, methionine is incorporated into the N-terminal position of all proteins in eukaryotes during translation, although it is usually removed by post-translational modification ,
so u can identify the RIGHT= ORF by this AUG in the start and that it doesnt have a stop codon in the middle , it will be the longest of the 3 reading frame i mentioned before.
hope this help.
.Any reading frame which does not contain a stop codon is known as an open reading frame.
hope this help.
yes it helps..
i already know the story of 6 reading frames, but what i just know now is why ORFs are called open..
...but eventually they will end with a stop codon ..right? what makes me soo confused is if you have a long DNA sequence and no web tool to find ORFs, what are you going to do? search for ATGs? also, it will be so hard to check for all 6 frames
for eukatyotes its sooo difficult to try it by urself without a web site.
ahhha, so it's easier for prokaryotes since they have no introns, right!
don't know how, but different tools i used gave me different number of ORFs