Inputsection-sequenceseqallAdditionalsection-beforeinteger
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.
-afterinteger
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.
-sourcestring
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: *
-typestring
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: *
-senseinteger
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
-minscorefloat
Minimum score of feature to extract (see also maxscore) Default value: 0.0
-maxscorefloat
Maximum score of feature to extract. If both minscore and maxscore are zero (the default), then any
score is ignored Default value: 0.0
-tagstring
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: *
-valuestring
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: *
Outputsection-joinboolean
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
-featinnameboolean
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
-describestring
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
-outseqseqout
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