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Old 06-08-2009, 11:40 PM   #1
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Location: delhi

Join Date: Jun 2009
Posts: 2
Default need help

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).
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."

Can anybody explain me
what this paragraph means i.e., from where I get these 3000 non-genes
bhatig is offline   Reply With Quote
Old 06-12-2009, 11:22 PM   #2
Location: Wuhan China

Join Date: Aug 2008
Posts: 13

I think the paragraph means that: the listed protein coding genes are consider as genes and the ones listed as ORFS are consider as non-genes in the training and testing. The genes and non-genes are come from NCBI GENBANK, the method to determine gene and non-gene are based the Genome annotation. But my question it's that: there are total 1610 genes in the analysis and the first 1000 genes was used as training set, so the number of the remain genes is 1610-1000=610, and how do the authors to get another 390 genes in the testing.
lry198010 is offline   Reply With Quote
Old 06-14-2009, 11:24 PM   #3
Junior Member
Location: delhi

Join Date: Jun 2009
Posts: 2

thanx for reply...i don't know answer of your question but will give as soon as i we are trying to contact the authors of the patent..plz do reply if you get something else..
bhatig is offline   Reply With Quote

e.coli, genes, non genes

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