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