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PROGRAM:
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
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