Provided by: emboss_6.6.0+dfsg-7_amd64 bug

NAME

       extractfeat - Extract features from sequence(s)

SYNOPSIS

       extractfeat -sequence seqall [-before integer] [-after integer] [-source string]
                   [-type string] [-sense integer] [-minscore float] [-maxscore float]
                   [-tag string] [-value string] [-join boolean] [-featinname boolean]
                   [-describe string] -outseq seqout

       extractfeat -help

DESCRIPTION

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

OPTIONS

   Input section
       -sequence seqall

   Additional section
       -before integer
           If this value is greater than 0 then that number of bases or residues before the
           feature are included in the extracted sequence. This allows you to get the context of
           the feature. If this value is negative then the start of the extracted sequence will
           be this number of bases/residues before the end of the feature. So a value of '10'
           will start the extraction 10 bases/residues before the start of the sequence, and a
           value of '-10' will start the extraction 10 bases/residues before the end of the
           feature. The output sequence will be padded with 'N' or 'X' characters if the sequence
           starts after the required start of the extraction.

       -after integer
           If this value is greater than 0 then that number of bases or residues after the
           feature are included in the extracted sequence. This allows you to get the context of
           the feature. If this value is negative then the end of the extracted sequence will be
           this number of bases/residues after the start of the feature. So a value of '10' will
           end the extraction 10 bases/residues after the end of the sequence, and a value of
           '-10' will end the extraction 10 bases/residues after the start of the feature. The
           output sequence will be padded with 'N' or 'X' characters if the sequence ends before
           the required end of the extraction.

       -source string
           By default any feature source in the feature table is shown. You can set this to match
           any feature source you wish to show. 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 show more
           than one source, separate their names with the character '|', eg: gene* | embl Default
           value: *

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

       -sense integer
           By default any feature type in the feature table is extracted. You can set this to
           match any feature sense you wish. 0 - any sense, 1 - forward sense, -1 - reverse sense

       -minscore float
           Minimum score of feature to extract (see also maxscore) Default value: 0.0

       -maxscore float
           Maximum score of feature to extract. If both minscore and maxscore are zero (the
           default), then any score is ignored Default value: 0.0

       -tag 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 extracted. You can set
           this to match any feature tag you wish to show. The tag may be wildcarded by using
           '*'. If you wish to extract more than one tag, separate their names with the character
           '|', eg: gene | label Default value: *

       -value 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 shown. You can set this to match any feature
           tag value you wish to show. The tag value may be wildcarded by using '*'. If you wish
           to show more than one tag value, separate their names with a space or the character
           '|', eg: pax* | 10 Default value: *

   Output section
       -join boolean
           Some features, such as CDS (coding sequence) and mRNA are composed of introns
           concatenated together. There may be other forms of 'joined' sequence, depending on the
           feature table. If this option is set TRUE, then any group of these features will be
           output as a single sequence. If the 'before' and 'after' qualifiers have been set,
           then only the sequence before the first feature and after the last feature are added.
           Default value: N

       -featinname boolean
           To aid you in identifying the type of feature that has been output, the type of
           feature is added to the start of the description of the output sequence. Sometimes the
           description of a sequence is lost in subsequent processing of the sequences file, so
           it is useful for the type to be a part of the sequence ID name. If you set this to be
           TRUE then the name is added to the ID name of the output sequence. Default value: N

       -describe string
           To aid you in identifying some further properties of a feature that has been output,
           this lets you specify one or more tag names that should be added to the output
           sequence Description text, together with their values (if any). For example, if this
           is set to be 'gene', then if any output feature has the tag (for example)
           '/gene=BRCA1' associated with it, then the text '(gene=BRCA1)' will be added to the
           Description line. 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 no feature tag is displayed. You can set this to match
           any feature tag you wish to show. The tag may be wildcarded by using '*'. If you wish
           to extract more than one tag, separate their names with the character '|', eg: gene |
           label

       -outseq seqout

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

       extractfeat 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.