Template - the template sequence is the nucleotide
sequence you want to view. Four formats are accepted:
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GenBank - the format used in the NIH (National Institutes of Health) sequence
database. View sample.
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EMBL - the format used in the EMBL (European Molecular Biology Laboratory)
sequence database. View sample.
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FASTA - consists of a single line description followed by sequence data.
The description line is marked by the > symbol, and the description is
followed by a carriage return. View sample.
-
Raw - consists only of sequence information. Non-IUPAC
codes are automatically removed. View sample.
Primers - the primer sequences are compared
to the template sequence and potential annealing sites are marked. Primer
sequences are entered as follows: the sequence of the primer is entered
first, followed by a blank space, and then the name of the primer. Primer
entries are separated by a comma. Degenerate
IUPAC
codes can be included in the primer sequence. "I" for inosine is treated
the same as "N".
Genetic code - the genetic code used
when translations are calculated for FASTA or raw entries.
Restriction set - the set of restriction
patterns searched for in the template sequence.
Translate reading frame - the reading frames
to be translated for FASTA or raw entries.
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one - show the translation for reading frame one.
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two -show the translation for reading frame two.
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three - show the translation for reading frame three.
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one to three - show the translation for reading frames one, two,
and three.
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all six - show the translations for all six reading frames.
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uppercase one - treat uppercase text as a continuous reading frame,
and start the translation in reading frame one.
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uppercase two - treat uppercase text as a continuous reading frame,
and start the translation in reading frame two.
-
uppercase three - treat uppercase text as a continuous reading frame,
and start the translation in reading frame three.
Topology - the topology of the sequence (linear
or circular). The distinction alters how restriction patterns and primer
sites are found. With linear sequences, the search is performed using the
sequence as entered. For circular sequences, the end and beginning of the
sequence are joined so that patterns spanning the ends of the entered sequence
can be detected.
Allow primers to have mismatched:
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5' tails - detect primer sites in which
the 5' tail of the primer contains bases that do not perfectly anneal with
the template.
-
3' tails - detect primer sites in which
the 3' tail of the primer contains bases that do not perfectly anneal with
the template.
Matching bases required when mismatching
bases allowed - when mismatching 5' tails or 3' tails are allowed,
this option sets the minimum number of annealing bases required for a primer
site to be detected.
Bases per line - the number of bases
of template sequence shown per line in the returned figure.
Show - use these options to adjust the appearence
of the sequence portion of the figure:
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Reverse strand - display the reverse
strand of the template sequence.
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Number line - display a line indicating
base number below the template sequence.
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Spacer line - display a line of dashes
between each line of template sequence.
Return - use these options to adjust what extra
information is returned with the sequence figure.
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Restriction summary - display a summary of
restriction patterns searched for, and the positions of restriction sites
when found.
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Primer summary - display a summary of primer
patterns searched for, and the positions of primer sites when found.
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Help information - display a brief description
of how to interpret and use the returned figure.
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Coding sequence links - display a group
of links for viewing the coding sequences of the template in a separate
window.
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Translation links - display a group of
links for viewing the protein translations of the template sequence in
a separate window.
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Options selected - display a summary
of the options selected.
Sequence Extractor copyright © 2006 Paul Stothard
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