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cmsearch (version 1.1.4+galaxy0)
... global with respect to the query model and local with respect to the target database.
in the sequence database
in the sequence database
By default, the Durbin/Holmes optimal accuracy algorithm is used, which finds the alignment that maximizes the expected accuracy of all aligned residues.
This correction is not used during the HMM filter stages.
These options are, in order from least strict (slowest but most sensitive) to most strict (fastest but least sensitive)
Options controlling model-specific reporting thresholds
Options controlling model-specific reporting thresholds 0
Inclusion thresholds are stricter than reporting thresholds. Inclusion thresholds control which hits are considered to be reliable enough to be included in an output alignment or in a possible subsequent search round, or marked as significant (”!”) as opposed to questionable (”?”) in hit output.
Reporting thresholds control which hits are reported in output files
... those satisfying inclusion thresholds
This can greatly reduce the output volume
They include filter survival statistics for truncated hit detection and number of envelopes discarded due to matrix size overflows.

What it does

cmsearch belongs to the INFERNAL software package that allows you to make consensus RNA secondary structure profiles, and use them to search nucleic acid sequence databases for homologous RNAs, or to create new structure-based multiple sequence alignments. You can use your model to search for new homologues of your RNA family. cmsearch is used to search one or more covariance models (CMs) against a sequence database. cmsearch searches both strands of each sequence in the target database, and returns alignments for high scoring hits.

To build CMs from multiple alignments, see cmbuild (build covariance models).


The CM query file must have been calibrated for E-values with cmcalibrate. As a special exception, any models CM query files that have zero basepairs need not be calibrated.


Output Options

Output columns:

  1. rank
  2. E-value
  3. score
  4. bias
  5. sequence
  6. start
  7. end
  8. mdl
  9. trunc
  10. gc
  11. description

---- --------- ------ ----- ----------- ------- ------- --- ----- ---- -----------

! 1.3e-18 71.5 0.0 NC_013790.1 362026 361955 - cm no 0.50 Methanobrevibacter ruminantium M1

! 3.3e-18 70.2 0.0 NC_013790.1 2585265 2585193 - cm no 0.60 Methanobrevibacter ruminantium M1

For further questions please refere to the Infernal Userguide.