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EddyRivasLab / hmmer

HMMER: biological sequence analysis using profile HMMs
http://hmmer.org
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Clarification about e-values from hmmscan #265

Closed nattzy94 closed 1 year ago

nattzy94 commented 2 years ago

Hi,

I queried a fasta file of protein sequences against the pfam database using hmmscan web application. I am a little confused about the difference between individual e-value vs. the full sequence e-value.

From the documents, it says that the independent e-value (I assume this means individual e-value) measures the significance of the sequence in the whole database search. It goes on to say that "If this E-value is not good, but the full sequence E-value is good, this is a potential red flag."

I am confused as it seems that the individual e-value already measures the significance of the sequence. Why is there another e-value for the full sequence? Is it perhaps referring to the sub-sequence that aligned to the model?

Also, is it possible to obtain the full sequence e-value using the web interface? I do not see it in the output of either in the batch or individual searches.

Thank you!

cryptogenomicon commented 1 year ago

(We think this is already explained in the User's Guide and other documentation.)