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

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

AUTHOR

Debian Med Packaging Team <[email protected]>

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.