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Old 12-07-2011, 01:34 PM   #1
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Location: Germany

Join Date: Dec 2011
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Default Using profile HMMs (HMMER) to annotate genomes

Dear community,

I didn't find a direct answer to my question. I am planning to annotate a huge bunge of genomes and metagenomes with profile HMMs like Pfam (also some custom models).

Because of the large size of the data set, I won't be able to optimize individual alignments of the HMMs and I am looking for a good set of parameters for hmmsearch (inclusion parameters) and postprocessing thresholds for e-values and coverage values, i.e. length of the match with respect to the length of the domain model. Could you please cite or tell me infos about finding values that are a good compromise!? And how would it be when processing some metagenomes?
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