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cmscan (version 1.1.2.0)
A tar file contains the four auxillury files suffixed .i1{fimp}. These files are generated after pressing the cm files using cmpress
... global with respect to the query model and local with respect to the target database.
Without the use of this option, the search space size changes for each query sequence
report extra information; mainly useful for debugging
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
Options controlling model-specific reporting thresholds
Options controlling model-specific reporting thresholds 0
These options are, in order from least strict (slowest but most sensitive) to most strict (fastest but least sensitive)
Other options
Other options 0

What it does

cmscan is used to search sequences against collections of covariance models. For each sequence in <seqfile>, use that query sequence to search the target database of CMs in <cmdb>, and output ranked lists of the CMs with the most significant matches to the sequence

Input format

The <seqfile> may contain more than one query sequence. It can be in FASTA format, or several other common sequence file formats (genbank, embl, and among others), or in alignment file formats (stockholm, aligned fasta, and others).

The <cmdb> needs to be press’ed using cmpress before it can be searched with cmscan. This creates four binary files, suffixed .i1{fimp}. Additionally, <cmdb> must have been calibrated for E-values with cmcalibrate before being press’ed with cmpress.

NOTE: Please provid a tar file that contains the .cm file in addition to the four binary files, suffixed .i1{fimp}, and specify the file type as "tar" before uploading the file. Otherwise Galaxy will not read the binary files properly.

Output format

The output format is designed to be human-readable.

For further questions please refere to the Infernal Userguide.