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.