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May 17th, 2024: NPS@ updated (see NEWS).


HMMER 3 PROFILE HMM HMMBUILD

[Abstract] [NPS@ help] [Original server]

Paste a multiple protein alignment in Clustal W format below : help

Restrict profile HMM HMMBUILD to multiple sequence alignment boundaries : from column to

Profile HMM HMMBUILD options :
Alternative model construction strategies (only --fast supported):
- Symbol fraction in each MSA column (--symfrac, 0<x<1):
- Fraction of MSA columns to tag sequence as fragment (--fragthresh, L <= x*alen, 0<x<1):

Alternative relative sequence weighting strategies: (--wgiven not supported)
- Henikoff simple filter weighting strategy (--wblosum): identity cutoff (--wid, 0<x<1)

Alternative effective sequence number strategies:
- eff seq # to achieve relative entropy target (-eent): minimum relative entropy/position (--ere) (bits/position), sigma param (--esigma):
- eff seq # is # of single linkage clusters (--eclust): fractional identity cutoff (--eid, 0<x<1):
- eff seq # for all models (--eset):

Alternative prior strategies:

Control of E-value calibration:
- MSV Gumbel mu fit: length of sequences (--EmL) , number of sequences (--EmN)
- Viterbi Gumbel mu fit: length of sequences (--EvL) , number of sequences (--EvN)
- Forward exp tail tau fit : length of sequences (--EfL) , number of sequences (--EfN) , tail mass (--Eft,0<x<1)

Other options:
- Seed (--seed):
- Inserts length (--maxinsertlen)


Last modification time : Fri Dec 8 17:26:06 2023. Current time : Sun May 19 09:08:49 2024. User : public@44.221.70.232.

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