domainalign - Generate alignments (DAF file) for nodes in a DCF file.

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DOMALIGN 0.1.0+20100721                            08/11/2010                                    DOMAINALIGN(1e)

domainalign is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”).
       It is part of the "Protein:3D Structure" command group(s).

       domainalign - Generate alignments (DAF file) for nodes in a DCF file.

Inputsection-dcfinfileinfile
           This option specifies the name of DCF file (domain classification file) (input). A 'domain
           classification file' contains classification and other data for domains from SCOP or CATH, in DCF
           format (EMBL-like). The files are generated by using SCOPPARSE and CATHPARSE. Domain sequence
           information can be added to the file by using DOMAINSEQS.

       -pdbdirdirectory
           This option specifies the location of domain PDB files (input). A 'domain PDB file' contains
           coordinate data for a single domain from SCOP or CATH, in PDB format. The files are generated by
           using DOMAINER. Default value: ./

   Requiredsection-nodelist
           This option specifies the node for redundancy removal. Redundancy can be removed at any specified
           node in the SCOP or CATH hierarchies. For example by selecting 'Class' entries belonging to the same
           Class will be non-redundant. Default value: 1

       -modelist
           This option specifies the alignment algorithm to use. Default value: 1

       -keepsingletstoggle
           This option specifies whether to write sequences of singlet families to file. If you specify this
           option, the sequence for each singlet family are written to file (output). Default value: Y

   Outputsection-dafoutdiroutdir
           This option specifies the location of DAF files (domain alignment files) (output). A 'domain
           alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family.
           The files are in clustal format and are annotated with domain family classification information. The
           files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of
           known structure only. Such alignments can be extended with sequence relatives (of unknown structure)
           by using SEQALIGN. Default value: ./

       -singletsoutdiroutdir
           This option specifies the location of DHF files (domain hits files) for singlet sequences (output).
           The singlets are written out as a 'domain hits file' - which contains database hits (sequences) with
           domain classification information, in FASTA format. Default value: ./

       -superoutdiroutdir
           This option specifies the location of structural superimposition files (output). A file in PDB format
           of the structural superimposition is generated for each family if the STAMP algorithm is used.
           Default value: ./

       -logfileoutfile
           This option specifies the name of log file (output). The log file contains messages about any errors
           arising while domainalign ran. Default value: domainalign.log

       domainalign is fully documented via the tfm(1) system.

domainalign-dcfinfileinfile-pdbdirdirectory-nodelist-modelist-keepsingletstoggle-dafoutdiroutdir-singletsoutdiroutdir-superoutdiroutdir-logfileoutfiledomainalign-help