]> Finds neighbouring pairs of features in sequences (EMBOSS) feature tables http://bioweb.pasteur.fr/docs/EMBOSS/twofeat.html twofeat &emboss_init; input Input section sequence sequence -- any [sequences] (-sequence) perl " -sequence=$value" 1 any 2 4 14 seqsfile perl 1 afeaturesection First feature options asource Source of first feature (-asource) all perl ($value && $value =~ s/all/*/)? " -asource=$value" : "" 2 By default any feature source in the feature table is allowed. You can set this to match any feature source you wish to allow. <BR> 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. <BR> The source may be wildcarded by using '*'. <BR> If you wish to allow more than one source, separate their names with the character '|', eg: <BR> gene* | embl atype Type of first feature (-atype) all perl ($value && $value =~ s/all/*/)? " -atype=$value" : "" 3 By default every feature in the feature table is allowed. You can set this to be any feature type you wish to allow. <BR> See http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.ch/txt/userman.txt for a list of the Swissprot feature types. <BR> The type may be wildcarded by using '*'. <BR> If you wish to allow more than one type, separate their names with the character '|', eg: <BR> *UTR | intron asense Sense of first feature -- Sense of first feature (-asense) 0 Any sense + Forward sense - Reverse sense 0 perl " -asense=$value" 4 By default any feature sense is allowed. You can set this to match the required sense. aminscore Minimum score of first feature (-aminscore) 0.0 perl (defined $value && $value != $vdef)? " -aminscore=$value" : "" 5 If this is greater than or equal to the maximum score, then any score is allowed. amaxscore Maximum score of first feature (-amaxscore) 0.0 perl (defined $value && $value != $vdef)? " -amaxscore=$value" : "" 6 If this is less than or equal to the maximum score, then any score is permitted. atag Tag of first feature (-atag) all perl ($value && $value =~ s/all/*/)? " -atag=$value" : "" 7 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. <BR> By default any feature tag in the feature table is allowed. You can set this to match any feature tag you wish to allow. <BR> The tag may be wildcarded by using '*'. <BR> If you wish to allow more than one tag, separate their names with the character '|', eg: <BR> gene | label avalue Value of first feature's tags (-avalue) all perl ($value && $value =~ s/all/*/)? " -avalue=$value" : "" 8 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. <BR> The tag value may be wildcarded by using '*'. <BR> If you wish to allow more than one tag value, separate their names with the character '|', eg: <BR> pax* | 10 bfeaturesection Second feature options bsource Source of second feature (-bsource) all perl ($value && $value =~ s/all/*/)? " -bsource=$value" : "" 9 By default any feature source in the feature table is allowed. You can set this to match any feature source you wish to allow. <BR> 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. <BR> The source may be wildcarded by using '*'. <BR> If you wish to allow more than one source, separate their names with the character '|', eg: <BR> gene* | embl btype Type of second feature (-btype) all perl ($value && $value =~ s/all/*/)? " -btype=$value" : "" 10 By default every feature in the feature table is allowed. You can set this to be any feature type you wish to allow. <BR> See http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.ch/txt/userman.txt for a list of the Swissprot feature types. <BR> The type may be wildcarded by using '*'. <BR> If you wish to allow more than one type, separate their names with the character '|', eg: <BR> *UTR | intron bsense Sense of second feature -- Sense of second feature (-bsense) 0 Any sense + Forward sense - Reverse sense 0 perl " -bsense=$value" 11 By default any feature sense is allowed. You can set this to match the required sense. bminscore Minimum score of second feature (-bminscore) 0.0 perl (defined $value && $value != $vdef)? " -bminscore=$value" : "" 12 If this is greater than or equal to the maximum score, then any score is allowed. bmaxscore Maximum score of second feature (-bmaxscore) 0.0 perl (defined $value && $value != $vdef)? " -bmaxscore=$value" : "" 13 If this is less than or equal to the maximum score, then any score is permitted. btag Tag of second feature (-btag) all perl ($value && $value =~ s/all/*/)? " -btag=$value" : "" 14 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. <BR> By default any feature tag in the feature table is allowed. You can set this to match any feature tag you wish to allow. <BR> The tag may be wildcarded by using '*'. <BR> If you wish to allow more than one tag, separate their names with the character '|', eg: <BR> gene | label bvalue Value of second feature's tags (-bvalue) all perl ($value && $value =~ s/all/*/)? " -bvalue=$value" : "" 15 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. <BR> The tag value may be wildcarded by using '*'. <BR> If you wish to allow more than one tag value, separate their names with the character '|', eg: <BR> pax* | 10 featurerelationsection Feature relation options overlap Specify overlap -- Type of overlap required (-overlap) A Any O Overlap required NO No overlaps are allowed NW Overlap required but not within AW A must be all within B BW B must be all within A A perl " -overlap=$value" 16 This allows you to specify the allowed overlaps of the features A and B. <BR> 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. minrange The minimum distance between the features (-minrange) 0 perl (defined $value && $value != $vdef)? " -minrange=$value" : "" 17 If this is greater or equal to 'maxrange', then no min or max range is specified maxrange The maximum distance between the features (-maxrange) 0 perl (defined $value && $value != $vdef)? " -maxrange=$value" : "" 18 If this is less than or equal to 'minrange', then no min or max range is specified rangetype Specify position -- Positions from which to measure the distance (-rangetype) N From nearest ends L From left ends R From right ends F From furthest ends N perl " -rangetype=$value" 19 This allows you to specify the positions from which the allowed minimum or maximum distance between the features is measured sense Specify sense -- Sense of the features (-sense) A Any sense S Same sense O Opposite sense A perl " -sense=$value" 20 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. order Specify order -- Order of the features (-order) A Any AB Feature A then feature B BA Feature B then feature A A perl " -order=$value" 21 This allows you to specify the required order of the two features. The order is measured from the start positions of the features. This criterion is always applied despite the specified overlap type required. output Output section twoout Do you want the two features written out individually (-twoout) 0 perl ($value)? " -twoout" : "" 22 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. typeout Name of the output new feature (-typeout) misc_feature perl ($value && $value ne $vdef)? " -typeout=$value" : "" 23 If you have specified that the pairs of features that are found should be reported as one feature in the ouput, then you can specify the 'type' name of the new feature here. By default every feature in the feature table is allowed. See http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.ch/txt/userman.txt for a list of the Swissprot feature types. If you specify an invalid feature type name, then the default name 'misc_feature' is used. outfile outfile (-outfile) outfile.out perl " -outfile=$value" 24 auto perl " -auto -stdout" 26