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.\"     Title: DOMAINALIGN
.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
.\"      Date: 08/11/2010
.\"    Manual: EMBOSS Manual for Debian
.\"    Source: DOMALIGN 0.1.0+20100721
.\"  Language: English
.\"
.TH "DOMAINALIGN" "1e" "08/11/2010" "DOMALIGN 0.1.0+20100721" "EMBOSS Manual for Debian"
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.SH "NAME"
domainalign \- Generate alignments (DAF file) for nodes in a DCF file\&.
.SH "SYNOPSIS"
.HP \w'\fBdomainalign\fR\ 'u
\fBdomainalign\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR \fB\-pdbdir\ \fR\fB\fIdirectory\fR\fR \fB\-node\ \fR\fB\fIlist\fR\fR \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-keepsinglets\ \fR\fB\fItoggle\fR\fR \fB\-dafoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-singletsoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-superoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
.HP \w'\fBdomainalign\fR\ 'u
\fBdomainalign\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBdomainalign\fR
is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:3D Structure" command group(s)\&.
.SH "OPTIONS"
.SS "Input section"
.PP
\fB\-dcfinfile\fR \fIinfile\fR
.RS 4
This option specifies the name of DCF file (domain classification file) (input)\&. A \*(Aqdomain classification file\*(Aq 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\&.
.RE
.PP
\fB\-pdbdir\fR \fIdirectory\fR
.RS 4
This option specifies the location of domain PDB files (input)\&. A \*(Aqdomain PDB file\*(Aq contains coordinate data for a single domain from SCOP or CATH, in PDB format\&. The files are generated by using DOMAINER\&. Default value: \&./
.RE
.SS "Required section"
.PP
\fB\-node\fR \fIlist\fR
.RS 4
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 \*(AqClass\*(Aq entries belonging to the same Class will be non\-redundant\&. Default value: 1
.RE
.PP
\fB\-mode\fR \fIlist\fR
.RS 4
This option specifies the alignment algorithm to use\&. Default value: 1
.RE
.PP
\fB\-keepsinglets\fR \fItoggle\fR
.RS 4
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
.RE
.SS "Output section"
.PP
\fB\-dafoutdir\fR \fIoutdir\fR
.RS 4
This option specifies the location of DAF files (domain alignment files) (output)\&. A \*(Aqdomain alignment file\*(Aq 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: \&./
.RE
.PP
\fB\-singletsoutdir\fR \fIoutdir\fR
.RS 4
This option specifies the location of DHF files (domain hits files) for singlet sequences (output)\&. The singlets are written out as a \*(Aqdomain hits file\*(Aq \- which contains database hits (sequences) with domain classification information, in FASTA format\&. Default value: \&./
.RE
.PP
\fB\-superoutdir\fR \fIoutdir\fR
.RS 4
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: \&./
.RE
.PP
\fB\-logfile\fR \fIoutfile\fR
.RS 4
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
.RE
.SH "BUGS"
.PP
Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
.SH "SEE ALSO"
.PP
domainalign is fully documented via the
\fBtfm\fR(1)
system\&.
.SH "AUTHOR"
.PP
\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
.SH "COPYRIGHT"
.br
.PP
This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
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