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.

EMBOSS 6.4.0                                       05/11/2012                                        TWOFEAT(1e)