]> REMAP Display a sequence with restriction cut sites, translation etc.. (EMBOSS) display nucleic:restriction nucleic:translation http://bioweb.pasteur.fr/docs/EMBOSS/remap.html remap &emboss_init; input Input section sequence sequence -- DNA [sequences] (-sequence) perl " -sequence=$value -sformat=fasta" 1 dna 8 seqsfile perl 1 required Required section enzymes Comma separated enzyme list (-enzymes) all perl " -enzymes=$value" 2 The name 'all' reads in all enzyme names from the REBASE database. You can specify enzymes by giving their names with commas between then, such as: 'HincII,hinfI,ppiI,hindiii'. <BR> The case of the names is not important. You can specify a file of enzyme names to read in by giving the name of the file holding the enzyme names with a '\@' character in front of it, for example, '\@enz.list'. <BR> Blank lines and lines starting with a hash character or '!' are ignored and all other lines are concatenated together with a comma character ',' and then treated as the list of enzymes to search for. <BR> An example of a file of enzyme names is: <BR> ! my enzymes <BR> HincII, ppiII <BR> ! other enzymes <BR> hindiii <BR> HinfI <BR> PpiI sitelen Minimum recognition site length (-sitelen) 4 perl " -sitelen=$value" 3 This sets the minimum length of the restriction enzyme recognition site. Any enzymes with sites shorter than this will be ignored. 2 20 advanced Advanced section mincuts Minimum cuts per RE (-mincuts) 1 perl (defined $value && $value != $vdef)? " -mincuts=$value" : "" 4 This sets the minimum number of cuts for any restriction enzyme that will be considered. Any enzymes that cut fewer times than this will be ignored. 1 1000 maxcuts Maximum cuts per RE (-maxcuts) 2000000000 perl (defined $value && $value != $vdef)? " -maxcuts=$value" : "" 5 This sets the maximum number of cuts for any restriction enzyme that will be considered. Any enzymes that cut more times than this will be ignored. acd $mincuts 2000000000 single Force single site only cuts (-single) 0 perl ($value)? " -single" : "" 6 If this is set then this forces the values of the mincuts and maxcuts qualifiers to both be 1. Any other value you may have set them to will be ignored. blunt Allow blunt end cutters (-blunt) 1 perl ($value)? "" : " -noblunt" 7 This allows those enzymes which cut at the same position on the forward and reverse strands to be considered. sticky Allow sticky end cutters (-sticky) 1 perl ($value)? "" : " -nosticky" 8 This allows those enzymes which cut at different positions on the forward and reverse strands, leaving an overhang, to be considered. ambiguity Allow ambiguous matches (-ambiguity) 1 perl ($value)? "" : " -noambiguity" 9 This allows those enzymes which have one or more 'N' ambiguity codes in their pattern to be considered plasmid Allow circular DNA (-plasmid) 0 perl ($value)? " -plasmid" : "" 10 If this is set then this allows searches for restriction enzyme recognition site and cut postions that span the end of the sequence to be considered. commercial Only enzymes with suppliers (-commercial) 1 perl ($value)? "" : " -nocommercial" 11 If this is set, then only those enzymes with a commercial supplier will be searched for. This qualifier is ignored if you have specified an explicit list of enzymes to search for, rather than searching through 'all' the enzymes in the REBASE database. It is assumed that, if you are asking for an explicit enzyme, then you probably know where to get it from and so all enzymes names that you have asked to be searched for, and which cut, will be reported whether or not they have a commercial supplier. table Genetic code to use -- Genetic codes (-table) 0 1 2 3 4 5 6 9 10 11 12 13 14 15 16 21 22 23 0 perl " -table=$value" 12 output Output section outfile outfile (-outfile) outfile.out perl " -outfile=$value" 13 cutlist List the enzymes that cut (-cutlist) 1 perl ($value)? "" : " -nocutlist" 14 This produces lists in the output of the enzymes that cut, those that cut but are excluded because that cut fewer times than mincut or more times than maxcut and those enzymes that do not cut. flatreformat Display RE sites in flat format (-flatreformat) 0 perl ($value)? " -flatreformat" : "" 15 This changes the output format to one where the recognition site is indicated by a row of '===' characters and the cut site is pointed to by a '>' character in the forward sense, or a '<' in the reverse sense strand. limit Limits reports to one isoschizomer (-limit) 1 perl ($value)? "" : " -nolimit" 16 This limits the reporting of enzymes to just one enzyme from each group of isoschizomers. The enzyme chosen to represent an isoschizomer group is the prototype indicated in the data file 'embossre.equ', which is created by the program 'rebaseextract'. If you prefer different prototypes to be used, make a copy of embossre.equ in your home directory and edit it. If this value is set to be false then all of the input enzymes will be reported. You might like to set this to false if you are supplying an explicit set of enzymes rather than searching 'all' of them. translation Display translation (-translation) 1 perl ($value)? "" : " -notranslation" 17 This displays the 6-frame translations of the sequence in the output. reverse Display cut sites and translation of reverse sense (-reverse) 1 perl ($value)? "" : " -noreverse" 18 This displays the cut sites and translation of the reverse sense. orfminsize Minimum size of ORFs (-orfminsize) 0 perl (defined $value && $value != $vdef)? " -orfminsize=$value" : "" 19 This sets the minimum size of Open Reading Frames (ORFs) to display in the translations. All other translation regions are masked by changing the amino acids to '-' characters. uppercase Regions to put in uppercase (eg: 4-57,78-94) (-uppercase) perl ($value)? " -uppercase=$value" : "" 20 Regions to put in uppercase. <BR> If this is left blank, then the sequence case is left alone. <BR> A set of regions is specified by a set of pairs of positions. <BR> The positions are integers. <BR> They are separated by any non-digit, non-alpha character. <BR> Examples of region specifications are: <BR> 24-45, 56-78 <BR> 1:45, 67=99;765..888 <BR> 1,5,8,10,23,45,57,99 highlight Regions to colour in HTML (eg: 4-57 red 78-94 green) (-highlight) perl ($value)? " -highlight=$value" : "" 21 Regions to colour if formatting for HTML. <BR> If this is left blank, then the sequence is left alone. <BR> A set of regions is specified by a set of pairs of positions. <BR> The positions are integers. <BR> They are followed by any valid HTML font colour. <BR> Examples of region specifications are: <BR> 24-45 blue 56-78 orange <BR> 1-100 green 120-156 red <BR> A file of ranges to colour (one range per line) can be specifed as '\@filename'. threeletter Display protein sequences in three-letter code (-threeletter) 0 perl ($value)? " -threeletter" : "" 22 number Number the sequences (-number) 0 perl ($value)? " -number" : "" 23 width Width of sequence to display (-width) 60 perl (defined $value && $value != $vdef)? " -width=$value" : "" 24 1 length Line length of page (0 for indefinite) (-length) 0 perl (defined $value && $value != $vdef)? " -length=$value" : "" 25 margin Margin around sequence for numbering (-margin) 10 perl (defined $value && $value != $vdef)? " -margin=$value" : "" 26 name Display sequence ID (-name) 1 perl ($value)? "" : " -noname" 27 Set this to be false if you do not wish to display the ID name of the sequence description Display description (-description) 1 perl ($value)? "" : " -nodescription" 28 Set this to be false if you do not wish to display the description of the sequence offset Offset to start numbering the sequence from (-offset) 1 perl (defined $value && $value != $vdef)? " -offset=$value" : "" 29 html Use HTML formatting (-html) 0 perl ($value)? " -html" : "" 30 auto perl " -auto -stdout" 31