NAME

       twofeat - Finds neighbouring pairs of features in sequence(s)

SYNOPSIS

       twofeat -sequence seqall [-asource string] -atype string [-asense list] [-aminscore float]
               [-amaxscore float] [-atag string] [-avalue string] [-bsource string] -btype string
               [-bsense list] [-bminscore float] [-bmaxscore float] [-btag string]
               [-bvalue string] [-overlap list] -minrange integer -maxrange integer
               [-rangetype list] [-sense list] [-order list] [-twoout toggle] -typeout string
               -outfile report

       twofeat -help

DESCRIPTION

       twofeat is a command line program from EMBOSS (“the European Molecular Biology Open
       Software Suite”). It is part of the "Feature tables" command group(s).

OPTIONS

   Input section
       -sequence seqall

   First feature options
       -asource string
           By default any feature source in the feature table is allowed. You can set this to
           match any feature source you wish to allow. The source name is usually either the name
           of the program that detected the feature or it is the feature table (eg: EMBL) that
           the feature came from. The source may be wildcarded by using '*'. If you wish to allow
           more than one source, separate their names with the character '|', eg: gene* | embl
           Default value: *

       -atype string
           By default every feature in the feature table is allowed. You can set this to be any
           feature type you wish to allow. See http://www.ebi.ac.uk/embl/WebFeat/ for a list of
           the EMBL feature types and see Appendix A of the Swissprot user manual in
           http://www.expasy.org/sprot/userman.html for a list of the Swissprot feature types.
           The type may be wildcarded by using '*'. If you wish to allow more than one type,
           separate their names with the character '|', eg: *UTR | intron Default value: *

       -asense list
           By default any feature sense is allowed. You can set this to match the required sense.

       -aminscore float
           If this is greater than or equal to the maximum score, then any score is allowed.
           Default value: 0.0

       -amaxscore float
           If this is less than or equal to the maximum score, then any score is permitted.
           Default value: 0.0

       -atag string
           Tags are the types of extra values that a feature may have. For example in the EMBL
           feature table, a 'CDS' type of feature may have the tags '/codon', '/codon_start',
           '/db_xref', '/EC_number', '/evidence', '/exception', '/function', '/gene', '/label',
           '/map', '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo',
           '/standard_name', '/translation', '/transl_except', '/transl_table', or '/usedin'.
           Some of these tags also have values, for example '/gene' can have the value of the
           gene name. By default any feature tag in the feature table is allowed. You can set
           this to match any feature tag you wish to allow. The tag may be wildcarded by using
           '*'. If you wish to allow more than one tag, separate their names with the character
           '|', eg: gene | label Default value: *

       -avalue string
           Tag values are the values associated with a feature tag. Tags are the types of extra
           values that a feature may have. For example in the EMBL feature table, a 'CDS' type of
           feature may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number',
           '/evidence', '/exception', '/function', '/gene', '/label', '/map', '/note', '/number',
           '/partial', '/product', '/protein_id', '/pseudo', '/standard_name', '/translation',
           '/transl_except', '/transl_table', or '/usedin'. Only some of these tags can have
           values, for example '/gene' can have the value of the gene name. By default any
           feature tag value in the feature table is allowed. You can set this to match any
           feature tag value you wish to allow. The tag value may be wildcarded by using '*'. If
           you wish to allow more than one tag value, separate their names with the character
           '|', eg: pax* | 10 Default value: *

   Second feature options
       -bsource string
           By default any feature source in the feature table is allowed. You can set this to
           match any feature source you wish to allow. The source name is usually either the name
           of the program that detected the feature or it is the feature table (eg: EMBL) that
           the feature came from. The source may be wildcarded by using '*'. If you wish to allow
           more than one source, separate their names with the character '|', eg: gene* | embl
           Default value: *

       -btype string
           By default every feature in the feature table is allowed. You can set this to be any
           feature type you wish to allow. See http://www.ebi.ac.uk/embl/WebFeat/ for a list of
           the EMBL feature types and see Appendix A of the Swissprot user manual in
           http://www.expasy.org/sprot/userman.html for a list of the Swissprot feature types.
           The type may be wildcarded by using '*'. If you wish to allow more than one type,
           separate their names with the character '|', eg: *UTR | intron Default value: *

       -bsense list
           By default any feature sense is allowed. You can set this to match the required sense.

       -bminscore float
           If this is greater than or equal to the maximum score, then any score is allowed.
           Default value: 0.0

       -bmaxscore float
           If this is less than or equal to the maximum score, then any score is permitted.
           Default value: 0.0

       -btag string
           Tags are the types of extra values that a feature may have. For example in the EMBL
           feature table, a 'CDS' type of feature may have the tags '/codon', '/codon_start',
           '/db_xref', '/EC_number', '/evidence', '/exception', '/function', '/gene', '/label',
           '/map', '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo',
           '/standard_name', '/translation', '/transl_except', '/transl_table', or '/usedin'.
           Some of these tags also have values, for example '/gene' can have the value of the
           gene name. By default any feature tag in the feature table is allowed. You can set
           this to match any feature tag you wish to allow. The tag may be wildcarded by using
           '*'. If you wish to allow more than one tag, separate their names with the character
           '|', eg: gene | label Default value: *

       -bvalue string
           Tag values are the values associated with a feature tag. Tags are the types of extra
           values that a feature may have. For example in the EMBL feature table, a 'CDS' type of
           feature may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number',
           '/evidence', '/exception', '/function', '/gene', '/label', '/map', '/note', '/number',
           '/partial', '/product', '/protein_id', '/pseudo', '/standard_name', '/translation',
           '/transl_except', '/transl_table', or '/usedin'. Only some of these tags can have
           values, for example '/gene' can have the value of the gene name. By default any
           feature tag value in the feature table is allowed. You can set this to match any
           feature tag value you wish to allow. The tag value may be wildcarded by using '*'. If
           you wish to allow more than one tag value, separate their names with the character
           '|', eg: pax* | 10 Default value: *

   Feature relation options
       -overlap list
           This allows you to specify the allowed overlaps of the features A and B. You can allow
           any or no overlaps, specify that they must or must not overlap, that one must or must
           not be wholly enclosed within another feature. Default value: A

       -minrange integer
           If this is greater or equal to 'maxrange', then no min or max range is specified

       -maxrange integer
           If this is less than or equal to 'minrange', then no min or max range is specified

       -rangetype list
           This allows you to specify the positions from which the allowed minimum or maximum
           distance between the features is measured Default value: N

       -sense list
           This allows you to specify the required sense that the two features must be on. This
           is ignored (always 'Any') when looking at protein sequence features. Default value: A

       -order list
           This allows you to specify the required order of the two features. The order is
           measured from the start positions of the features. This criterion is always applied
           despite the specified overlap type required. Default value: A

   Output section
       -twoout toggle
           If you set this to be true, then the two features themselves will be written out. If
           it is left as false, then a single feature will be written out covering the two
           features you found. Default value: N

       -typeout string
           If you have specified that the pairs of features that are found should be reported as
           one feature in the output, then you can specify the 'type' name of the new feature
           here. By default every feature in the feature table is allowed. See
           http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL feature types and see
           Appendix A of the Swissprot user manual in http://www.expasy.org/sprot/userman.html
           for a list of the Swissprot feature types. If you specify an invalid feature type
           name, then the default name 'misc_feature' is used. Default value: misc_feature

       -outfile report

BUGS

       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).

SEE ALSO

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

AUTHOR

       Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
           Wrote the script used to autogenerate this manual page.

COPYRIGHT

       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.