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Old 02-23-2013, 05:04 AM   #1
pulikoti
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Location: Finland

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Default GLimmer: How does the module 'glimmer' use the model to find the putative genes

Hi all,

Can someone explain how Glimmer (gene prediction tool) uses the module 'glimmer' to find the putative genes, using the IMM model. How does it identify the orf in the new genome?
The articles explain mainly the selection of the training data used to build the model and the model itself. It is mentioned that the model is used to find putative orfs in the genome but no detailed explanation of the procedure . Can someone give me the details of the same or relevant articles? Kindly help. Thanks
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Old 02-24-2013, 08:59 PM   #2
krobison
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From the original paper: "it first identifies all orfs longer than some specified threshold value, and scores each one in all six reading frames. Those that score higher than a designated threshold in the correct reading frame are then selected for further processing".

the further processing is detailed in the first paper & then modified in the second paper, and largely concerns coping with overlapping reading frames.
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