Inputsection-sequenceseqallFirstfeatureoptions-asourcestring
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: *
-atypestring
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: *
-asenselist
By default any feature sense is allowed. You can set this to match the required sense.
-aminscorefloat
If this is greater than or equal to the maximum score, then any score is allowed. Default value: 0.0
-amaxscorefloat
If this is less than or equal to the maximum score, then any score is permitted. Default value: 0.0
-atagstring
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:
*
-avaluestring
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: *
Secondfeatureoptions-bsourcestring
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: *
-btypestring
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: *
-bsenselist
By default any feature sense is allowed. You can set this to match the required sense.
-bminscorefloat
If this is greater than or equal to the maximum score, then any score is allowed. Default value: 0.0
-bmaxscorefloat
If this is less than or equal to the maximum score, then any score is permitted. Default value: 0.0
-btagstring
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:
*
-bvaluestring
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: *
Featurerelationoptions-overlaplist
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
-minrangeinteger
If this is greater or equal to 'maxrange', then no min or max range is specified
-maxrangeinteger
If this is less than or equal to 'minrange', then no min or max range is specified
-rangetypelist
This allows you to specify the positions from which the allowed minimum or maximum distance between
the features is measured Default value: N
-senselist
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
-orderlist
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
Outputsection-twoouttoggle
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
-typeoutstring
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
-outfilereport
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