Network Protein Sequence Analysis (NPSA, NPS@) image
This site is a fork of the original PRABI NPS@ server


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


HMMER 3 PROFILE HMM HMMSEARCH

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

Database :

Paste a HMMER 3 profile HMM below : help
You can build a profile HMM with HMMBUILD.

Number of results to display :

Profile HMM HMMSEARCH options :
Options controlling reporting thresholds:
- Report sequences <= this E-value threshold (-E) :
   OR Report sequences >= this score threshold (-T) :
- Report domains <= this E-value threshold (--domE) :
   OR Report domains >= this score threshold (--domT) :

Options controlling inclusion (significance) thresholds:
- Include sequences <= this E-value threshold (--incE) :
   OR Include sequences >= this score threshold (--incT) :
- Include domains <= this E-value threshold (--incdomE) :
   OR Include domains >= this score threshold (--incdomT) :

Options controlling acceleration heuristics:
- Turn all heuristic filters off (--max) : (less speed, more power)
- P-value threshold for the MSV filter (Stage 1) step (--F1) : (roughly 2% of the highest scoring nonhomologous targets are expected to pass the filter)
- P-value threshold for the Viterbi filter (Stage 2) step (--F2) :
- P-value threshold for the Forward filter (Stage 3) step (--F3) :
- Turn off composition bias filter (--nobias) : (increases sensitivity somewhat, but can come at a high cost in speed, especially if the query has biased residue composition)

Other expert options:
- Turn off composition bias filter (--nonull2) :
- Set # of comparisons done, for per-sequence E-value calculations (-Z) :
- Set # of significant seqs, for per-domain conditional E-value calculations (--domZ) :
- Set the random number seed (--seed) : (if 0: one-time arbitrary seed)


Last modification time : Tue Apr 30 10:58:40 2024. Current time : Sun May 19 10:46:22 2024. User : public@44.221.70.232.

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