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gene prediction programs for prokaryotes

I run Orphelia and MetaGeneMark the results are a set of predicted genes.

How to compute accuracy of these programs( number of True positives, number of false positives and number of false negatives)?

gene
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updated by 5heikki 5heikki • written by Am.A • Am.A

1 answer

Unless you have rnaseq or proteomics data, you really can't, can you? To get an idea of prediction accuracy, you could run said programs on some refseq genomes and then compare the predictions to the actual annotations.

p.s. I'm a big fan of prodigal

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written by 5heikki 5heikki

Yes I use data sets that contain 400bp reads from E. coli genome. Is there a script to compare the predictions to the actual annotations?

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written by Am.A • Am.A

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