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.
- Turn on the glocal alignment algorithm: global with respect to the query model and local with respect to the target database. By default, the local alignment algorithm is used which is local with respect to both the target sequence and the model. In local mode, the alignment to span two or more subsequences if necessary (e.g. if the structures of the query model and target sequence are only partially shared), allowing certain large insertions and deletions in the structure to be penalized differently than normal indels. Local mode performs better on empirical benchmarks and is significantly more sensitive for remote homology detection. Empirically, glocal searches return many fewer hits than local searches, so glocal may be desired for some applications. With Turn on the glocal alignment algorithm, all models must be calibrated, even those with zero basepairs.
- Only search the bottom (Crick) strand of target sequences: Hits can occur on either the top (Watson) or bottom (Crick) strand of the target sequence. By default, both strands are searched.
- Only search the top (Watson) strand of target sequences: Hits can occur on either the top (Watson) or bottom (Crick) strand of the target sequence. By default, both strands are searched.
- Use the CYK algorithm, not Inside, to determine the final score of all hits: If selecting "yes", the CYK algorithm instead of the CM Inside algorithm (the SCFG analog of the HMM Forward algorithm) is used.
- Use the CYK algorithm to align hits: By default, the Durbin/Holmes optimal accuracy algorithm is used, which finds the alignment that maximizes the expected accuracy of all aligned residues.
- Turn off truncated hit detection: Turns off truncated hit detection and will reduce the running time most significantly for target files that include many short sequences.
- Turn off all filters, and run non-banded Inside on every full-length target sequence: This increases sensitivity somewhat, at an extremely large cost in speed.
- Turn off all HMM filter stages: The CYK filter, using QDBs, will be run on every full-length target sequence and will enforce a P-value threshold of 0.0001. Each subsequence that survives CYK will be passed to Inside, which will also use QDBs (but a looser set). This increases sensitivity somewhat, at a very large cost in speed.
- Turn off the HMM SSV and Viterbi filter stages:Sets remaining HMM filter thresholds to 0.02 by default. This may increase sensitivity, at a significant cost in speed.
- Inclusion thresholds: Use E-value - Use an E-value as the hit inclusion threshold. The default is 0.01, meaning that on average, about 1 false positive would be expected in every 100 searches with different query sequences. Use Bit Score - Instead of using E-values for setting the inclusion threshold, instead use a bit score as the hit inclusion threshold. By default this option is unset.
- reporting thresholds: Hits are ranked by statistical significance (E-value). By default, all hits with an E-value <= 10 are reported. The following options allow you to change the default E-value reporting thresholds, or to use bit score thresholds instead.
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! 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.