interpreting frahmer output

[dcopetti]

Hello, can you please describe or point me to a resource for understanding the tabular output of frahmmer? Especially for the less intuitive columns like env, bias, shifts, stops, pipe. Thanks, Dario

[GenevieveKrause]

We are still working on getting the documentation up.

The env columns refer to the full coordinates of the "envelope" which is the full region where frahmmer found the hit and may extend beyond the alignment coordinates.

Bias refers to an adjustment that is made to the score to account for low complexity and repetitive regions. You can ignore it unless it is on the same order of magnitude as the score, which may indicate a false positive.

Shifts and stops refer to the number of frameshifts and stop codons found in the alignment.

Pipe refers to which model frahmmer used to produce the final score, e-value, and alignment. Once frahmmer detects a potential homology it asks whether it is better explained under a standard translation model that does not allow frameshifts (listed as 'std') or the frameshift-aware model (listed as 'fs'). You don't need to pay much attention to this information and can instead just consider whether or not any frameshifts or stop codons were found.

I will be working on getting the documentation up soon, but in the meantime feel free to email me with any further questions