Web Map Preferences



Set FrequencyThe fields at right allow the user to specify the frequency of enzyme cleavage sites displayed in the map output. Yes No Sites Max Sites Minimum
Site Complexity:This field is used to reject enzymes that cut too frequently. Its value is the minimum number of basepairs in the enzyme recognition sequence, adjusted for ambiguity. For example, if the minimum is set to 6, enzymes that recognize unambiguous sequences less than 6 basepairs long, or that recognize a 6 basepair sequence with at least one ambiguous basepair, will not be included in the map. Integer values are not required.  >  Residues Reject coli methyl:If this switch is set to Yes, restriction sites that are predicted not to be cleaved because of overlapping E. coli dcm or dam methylation will not be included in the map or fragment list. Cleavage site resistance information is based on the enzyme providers' descriptions. Yes No
Header:This establishes the GenBank header fields to be displayed on page opening.  Locus
Refs Comment Features All
Show Variations:If this switch is set to Yes any variations (mutations, polymorphisms, sequence discrepancies) listed in a GenBank feature table will be highlighted in the sequence. The highlight color can be set by the Variation Highlight control. Yes No
Enzyme ChoicesThis field identifies enzymes that will be added to the map, overriding other controls. The names of the enzymes specified here will be given a distinct color (and/or appearance), as specified by the Selected Enzymes switch. Enzymes added to the map by default (as specified by the Site Complexity field) are highlighted in the Enzyme Picker. All enzyme names in the Enzyme Picker are hyperlinked to explanation windows. Checking a highlighted enzyme will change its color in the map. To display only specific enzymes, set the minimum complexity to some large number and then choose the desired enzymes from the picker. Enzymes can also be added to the text field directly.
Enzyme File:This button can be used to provide a local file containing data on the enzymes to be used. The file must have the same structure as the file "enzyme data" in subfolder /enz/ of this site.
Amino Acid OffsetThis field determines where the symbol for the amino acid is placed in the map. If set to 0, the single letter code will be placed under the middle nucleotide of the codon; if set to -1, the letter will be placed under the first nucleotide, etc. bp Minimum Orf Length:This field prevents the display of potential open reading frames having a length less than the specified number of basepairs. Basepairs
Start Residues:This field can be filled with letters representing the acceptable amino acids for the beginning of an open reading frame. A blank signifies any amino acid is acceptable. A common string for bacterial genes might be MVIL. Reject Overlapping Orfs:This switch allows or prevents the display of overlapping open reading frames from input sequences that do not conform to GenBank format. If set to Yes the longest open reading frame for any given region will exclude all smaller overlapping orfs. Yes No
Frames WantedThese checkboxes allow the predicted translations of the sequence to be included. By default the application does not attempt to identify open reading frames in GenBank pages, but defers to the translations identified in the GenBank page Features field. Otherwise the algorithm used to identify orfs consists of translating all frames and identifying the longest run of sequences that begin with an acceptable amino acid and end with a stop codon (this does not take initiation codon context into account). If overlapping open reading frames are not desired (the default in the corresponding preference switch) the orfs are then sorted by length and any that overlap with the longest are removed. The longest surviving orf is then chosen from the remaining list and the procedure repeated until no candidate orfs remain to be tested.
0 1 2 for all orf
-1 -2 -3 rev no gb+
Disambiguation Order:Translation products in GenBank feature tables can have multiple qualifiers. Some have a "gene=" qualifier, some a "product=", some a "note=", some a "name=", and some a "protein_id=" qualifier; combinations of these are also common. In addition, a gene can encode multiple translation products, which may lead to different open reading frames that share qualifiers. The fields shown here control the preference order for assigning tags to open reading frames, based on the qualifiers associated with that coding sequence. They also control the order in which GenBank features are composited to form an unambiguous translation tag (if needed).
Name Gene Product Note Protein
Left Spacing:This field controls the width of the left margin of the map, which contains the reading frame tags and sequence numbering. Characters Sequence Width:This field sets the number of basepairs displayed per line. Characters Per Line
Stack EnzymesThis field controls the maximum height to which enzyme names can be stacked above the displayed sequence. High Separator Template:This field can be used to override the default separator between the top and bottom lines of the displayed sequence. Whatever string is entered will be repeated throughout the sequence.
Page BackgroundThis field sets the background color of the map.
Unique Sites:This field sets the color used to highlight sites that appear only once in the sequence. Any red green blue hexadecimal code of the form #rrggbb, e.g. #9a80ff, can be entered (the hexadecimal digits are 0-9a-f).
Amino Acids:This field sets the color of the amino acid links. Any red green blue hexadecimal code of the form #rrggbb, e.g. #9a80ff, can be entered (the hexadecimal digits are 0-9a-f).
Variation Highlight:This field sets the highlight color (background color) of any sequence variation sites listed in the sequence feature table if the Show Variations switch is set to Yes.
Selected Enzymes:This field sets the color of the enzymes selected with the enzyme picker (or entered directly in the Enzyme Choices text box).
Translations:This field sets the font color of the translated sequence names. It also sets the font color for the end fragments of linear sequences, which may not correspond to physical fragments.
Sequence Color:This field sets the color of the sequence itself.
Show Timing:This switch sets the timing trace flag. The cpu time in seconds for the major program segments will be output in the map. In general the server will generate the map in much less time than it takes the browser to parse the output. Yes No
IE WarningThis switch controls whether the Internet Explorer warning message is displayed or not. To turn the warning off on future visits, select No and save your preferences. Yes No Page Block Size:This field controls the length of sequence analyzed in each pass. The default provides good performance for sequences under 250 kb. For very long sequences larger values will speed execution at the cost of memory; but eventually virtual memory overhead may limit execution speed. To explore the consequences of this for very long sequences it may be helpful to set the Show Timing flag.
Preferences:The save button allows the present values of the form to be stored. The reset button restores the page defaults without changing the stored preferences.
Cookie:This button causes the preferences cookie to be removed from your browser-specified cookie file, which will remove any saved preferences without changing the values entered in the form. This may be useful if the preferences form has changed since you last visited the site.
Formats   The supported formats include GenBank, GCG, extended FastA and raw sequence. GenBank+ allows additional reading frames to be appended. If protein sequence is entered a map showing all possible restriction sites allowed by the sequence will be displayed. The displayed sequence is then only a guide (actual sequence is branched). Circular   Default GenBank+




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