remap uses REBASE data to find the recognition sites and/or cut sites of restriction enzymes in a nucleic acid sequence. It also displays the cut sites on both strands by default. It will optionally also display the translation of the sequence. Here is a sample session with remap. We only look at a small section of the sequence to save space: % remap -notran -sbeg 1 -send 60 Display a sequence with restriction cut sites, translation etc.. Input sequence(s): embl:eclac Output file [eclac.remap]: Comma separated enzyme list [all]: taqi,bsu6i,acii,bsski Minimum recognition site length [4]: Here is an example where all enzymes in the REBASE database are used: % remap -notran -sbeg 1 -send 60 Display a sequence with restriction cut sites, translation etc.. Input sequence(s): embl:eclac Output file [eclac.remap]: Comma separated enzyme list [all]: Minimum recognition site length [4]: Mandatory qualifiers: - [-sequence] (seqall)
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Sequence database USA. - -enzymes (string)
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The argument all reads all enzyme names from the REBASE database. You can specify enzymes by giving their names with commas between them, such as: HincII,hinfI,ppiI,hindiii. This command is not case-sensitive. You may also use the data from file containing enzyme names by prepending the name of the file you want to use with an @ character; for example, @enz.list. Blank lines and lines starting with a comment tag (# or !) within the file are ignored; all other lines are concatenated together with a comma and treated as the list of enzymes to search for. A file containing enzyme names might look like this: ! my enzymes HincII, ppiII ! other enzymes hindiii HinfI PpiI - -sitelen (integer)
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Minimum recognition site length. - [-outfile] (outfile)
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If you enter the name of a file here, this program will write the sequence details into that file. Optional qualifiers: - -mincuts (integer)
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Minimum cuts per restriction enzyme. - -maxcuts (integer
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Maximum cuts per restriction enzyme. - -single (boolean)
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Force single-site-only cuts. - -[no]blunt (boolean)
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Allow blunt end cutters. - -[no]sticky (boolean)
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Allow sticky end cutters. - -[no]ambiguity (boolean)
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Allow ambiguous matches. - -plasmid (boolean)
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Allow circular DNA. - -[no]commercial (boolean)
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Only enzymes with suppliers. - -table (menu)
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Code to use. See the fuzztran description for codes. - -[no]cutlist (boolean)
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List the enzymes to cut. - -flatreformat (boolean)
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Display restriction enzyme sites in flat format. - -[no]limit (boolean)
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Limits reports to one isoschizomer. - -preferred (boolean)
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Report preferred isoschizomers. Advanced qualifiers: - -[no]translation (boolean)
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Display translation. - -[no]reverse (boolean)
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Display cut sites and translation of reverse sense. - -orfminsize (integer)
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Minimum size of Open Reading Frames (ORFs) to display in the translations. - -uppercase (range)
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Regions to put in uppercase. If no regions are specified, the sequence case is left alone. A set of regions is specified by a set of pairs of positions. The positions are integers. They are separated by any non-digit, non-alpha character. Examples of region specification: 24-45, 56-78, 1:45, 67=99;765..888, 1,5,8,10,23,45,57,99. - -highlight (range)
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Regions to color if formatting in HTML. If no regions are specified, the sequence is left alone. A set of regions is specified by a set of pairs of positions. The positions are integers. They are followed by any valid HTML font color. Examples of region specifications: 24-45 blue 56-78 orange 1-100 green 120-156 red A file of ranges to color (one range per line) can be specifed as @filename. - -threeletter (boolean)
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Display protein sequences in three-letter code. - -number (boolean)
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Number the sequences. - -width (integer)
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Width of sequence to display. - -length (integer)
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Line length of page (0 for indefinite length). - -margin (integer)
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Margin around sequence for numbering. - -[no]name (boolean)
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Set this to false if you do not want to display the ID name of the sequence. - -[no]description (boolean)
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Set this to false if you do not want to display the description of the sequence. - -offset (integer)
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Offset to start numbering the sequence from. - -html (boolean)
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Use HTML formatting. |