domainaligne - Online in the Cloud

PROGRAM:

NAME

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

SYNOPSIS

domainalign -dcfinfile infile -pdbdir directory -node list -mode list -keepsinglets toggle
-dafoutdir outdir -singletsoutdir outdir -superoutdir outdir -logfile outfile

domainalign -help

DESCRIPTION

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).

OPTIONS

Input section
-dcfinfile infile
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.

-pdbdir directory
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: ./

Required section
-node list
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

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

-keepsinglets toggle
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

Output section
-dafoutdir outdir
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: ./

-singletsoutdir outdir
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: ./

-superoutdir outdir
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: ./

-logfile outfile
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

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