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yatin.arora 06-08-2009 08:09 AM

what are non gene sequences
I was reading this patent which contained a training of a neural network the training set consisted of a set of genes and a set of non genes could you give me some information about non genes that is
1.what are non genes?
2. how can i get their sequences ?
3. what kind of organisms have high number of non genes?
4.are pseudo genes same as non genes?

Patent and Paragraph details
publication number :US 2005 /0136480 A1
publication date 23rd june 2005
paragraph no [0081]

paragraph text
"The training set' consists of 1610 E coli .K-12
NCBI listed protein coding genes and 3000 F. E coli .K-12
ORFS (a stretch of sequence of length more than 20 amino
acids and having start codon, stop codon in the same frame)
which have not been reported as genes (non-genes). The
validation set has 1000 known genes and 1000 non-genes
from E coli .K-12 distinct from those used in the training set.
The test set contains another 1000 genes and 1000 nongenes
from the same organism. For training of the ANN,
genes and the non-genes are assigned a probability value of
1 and 0 respectively
expecting a prompt reply
yatin arora

Kai31410 06-23-2009 09:10 AM

Re: what are non gene sequences
A gene is the basic unit of heredity in a living organism. All living things depend on genes. Genes hold the information to build and maintain their cells and pass genetic traits to offspring. In general terms, a gene is a segment of nucleic acid that, taken as a whole, specifies a trait. The colloquial usage of the term gene often refers to the scientific concept of an allele.

The notion of a gene has evolved with the science of genetics, which began when Gregor Mendel noticed that biological variations are inherited from parent organisms as specific, discrete traits. The biological entity responsible for defining traits was termed a gene, but the biological basis for inheritance remained unknown until DNA was identified as the genetic material in the 1940s. All organisms have many genes corresponding to many different biological traits, some of which are immediately visible, such as eye color or number of limbs, and some of which are not, such as blood type or increased risk for specific diseases, or the thousands of basic biochemical processes that comprise life.

Mathijs 06-24-2009 10:42 AM

Re: what are non gene sequences
Not everything that has a start codon and stopcodon in the same frame on the genome is actually a coding gene sequence. In non-coding junk DNA there will be sequences occuring that simply have a start and stop codon in frame by chance. The position in the genome and absence of regulatory sequences (such as promotors) will prevent such open reading frames from beeing expressed. They simply took 1000 of these open reading frames, (from which they know that they aren't expressed) and 1000 open reading frames of actual genes.

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