remap Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Display restriction enzyme binding sites in a nucleotide sequence Description remap scans one or more nucleotide sequences for recognition sites and/or cut sites for a supplied set of restriction enzymes. One or more restriction enzymes can be specified or alternatively all the enzymes in the REBASE database can be investigated. The minimum length of a recognition site to be reported must be specified. It writes an output file showing the location of the cut sites and (optionally) the recognition sites. Sites on both strands are shown by default but there are many options to control exactly what sites are reported and the format of the output file. Optionally, the translated sequence is reported. Additionally, the output file lists enzymess that cut / do not cut the sequence and which match / do not matching certain specified criteria. Usage Here is a sample session with remap This example uses only a small region of the input sequence to save space. This is run with a small test version of the restriction enzyme database and so you will probably see more enzymes when you run this. % remap -notran -sbeg 1 -send 60 Display restriction enzyme binding sites in a nucleotide sequence Input nucleotide sequence(s): tembl:j01636 Comma separated enzyme list [all]: taqi,bsu6i,acii,bsski Minimum recognition site length [4]: Output file [j01636.remap]: Go to the input files for this example Go to the output files for this example Example 2 This is an example where all enzymes in the REBASE database are used, (but only the prototypes of the isoschizomers are reported by default). This is run with a small test version of the restriction enzyme database and so you will probably see more enzymes when you run this. % remap -notran -sbeg 1 -send 60 Display restriction enzyme binding sites in a nucleotide sequence Input nucleotide sequence(s): tembl:j01636 Comma separated enzyme list [all]: Minimum recognition site length [4]: Output file [j01636.remap]: Go to the output files for this example Example 3 This is an example where all enzymes in the REBASE database are used but the -limit qualifier is not set so that all of the enzymes are displayed and not just only the prototypes of the isoschizomers. This is run with a small test version of the restriction enzyme database and so you will probably see more enzymes when you run this. % remap -notran -sbeg 1 -send 60 -nolimit Display restriction enzyme binding sites in a nucleotide sequence Input nucleotide sequence(s): tembl:j01636 Comma separated enzyme list [all]: Minimum recognition site length [4]: Output file [j01636.remap]: Go to the output files for this example Example 4 This shows the 'flat' format: This is run with a small test version of the restriction enzyme database and so you will probably see more enzymes when you run this. % remap -notran -sbeg 1 -send 60 -flat Display restriction enzyme binding sites in a nucleotide sequence Input nucleotide sequence(s): tembl:j01636 Comma separated enzyme list [all]: Minimum recognition site length [4]: Output file [j01636.remap]: Go to the output files for this example Command line arguments Display restriction enzyme binding sites in a nucleotide sequence Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] seqall Nucleotide sequence(s) filename and optional format, or reference (input USA) -enzymes string [all] 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'. 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'. 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. An example of a file of enzyme names is: ! my enzymes HincII, ppiII ! other enzymes hindiii HinfI PpiI (Any string) -sitelen integer [4] This sets the minimum length of the restriction enzyme recognition site. Any enzymes with sites shorter than this will be ignored. (Integer from 2 to 20) [-outfile] outfile [*.remap] Output file name Additional (Optional) qualifiers: -mincuts integer [1] 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. (Integer from 1 to 1000) -maxcuts integer [2000000000] 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. (Any integer value) -single boolean [N] 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. -[no]blunt boolean [Y] This allows those enzymes which cut at the same position on the forward and reverse strands to be considered. -[no]sticky boolean [Y] This allows those enzymes which cut at different positions on the forward and reverse strands, leaving an overhang, to be considered. -[no]ambiguity boolean [Y] This allows those enzymes which have one or more 'N' ambiguity codes in their pattern to be considered -plasmid boolean [N] If this is set then this allows searches for restriction enzyme recognition site and cut positions that span the end of the sequence to be considered. -methylation boolean [N] If this is set then RE recognition sites will not match methylated bases. -[no]commercial boolean [Y] 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 menu [0] Genetic code to use (Values: 0 (Standard); 1 (Standard (with alternative initiation codons)); 2 (Vertebrate Mitochondrial); 3 (Yeast Mitochondrial); 4 (Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma); 5 (Invertebrate Mitochondrial); 6 (Ciliate Macronuclear and Dasycladacean); 9 (Echinoderm Mitochondrial); 10 (Euplotid Nuclear); 11 (Bacterial); 12 (Alternative Yeast Nuclear); 13 (Ascidian Mitochondrial); 14 (Flatworm Mitochondrial); 15 (Blepharisma Macronuclear); 16 (Chlorophycean Mitochondrial); 21 (Trematode Mitochondrial); 22 (Scenedesmus obliquus); 23 (Thraustochytrium Mitochondrial)) -frame menu [6] This allows you to specify the frames that are translated. If you are not displaying cut sites on the reverse sense, then the reverse sense translations will not be displayed even if you have requested frames 4, 5 or 6. By default, all six frames will be displayed. (Values: 1 (1); 2 (2); 3 (3); F (Forward three frames); -1 (-1); -2 (-2); -3 (-3); R (Reverse three frames); 6 (All six frames)) -[no]cutlist boolean [Y] 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 boolean [N] 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. -[no]limit boolean [Y] 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. Advanced (Unprompted) qualifiers: -mfile datafile [Emethylsites.dat] Restriction enzyme methylation data file -[no]translation boolean [Y] This displays the 6-frame translations of the sequence in the output. -[no]reverse boolean [Y] This displays the cut sites and translation of the reverse sense. -orfminsize integer [If this value is left as 0 then all of the translation is shown.] 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. (Integer 0 or more) -uppercase range [If this is left blank, then the sequence case is left alone.] Regions to put in uppercase. If this is left blank, then 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 specifications are: 24-45, 56-78 1:45, 67=99;765..888 1,5,8,10,23,45,57,99 -highlight range [(full sequence)] Regions to colour if formatting for HTML. If this is left blank, then 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 colour. Examples of region specifications are: 24-45 blue 56-78 orange 1-100 green 120-156 red A file of ranges to colour (one range per line) can be specified as '@filename'. -threeletter boolean [N] Display protein sequences in three-letter code -number boolean [N] Number the sequences -width integer [60] Width of sequence to display (Integer 1 or more) -length integer [0] Line length of page (0 for indefinite) (Integer 0 or more) -margin integer [10] Margin around sequence for numbering (Integer 0 or more) -[no]name boolean [Y] Set this to be false if you do not wish to display the ID name of the sequence -[no]description boolean [Y] Set this to be false if you do not wish to display the description of the sequence -offset integer [1] Offset to start numbering the sequence from (Any integer value) -html boolean [N] Use HTML formatting Associated qualifiers: "-sequence" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each sequence to be used -sreverse1 boolean Reverse (if DNA) -sask1 boolean Ask for begin/end/reverse -snucleotide1 boolean Sequence is nucleotide -sprotein1 boolean Sequence is protein -slower1 boolean Make lower case -supper1 boolean Make upper case -sformat1 string Input sequence format -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-outfile" associated qualifiers -odirectory2 string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit Input file format Input files for usage example 'tembl:j01636' is a sequence entry in the example nucleic acid database 'tembl' Database entry: tembl:j01636 ID J01636; SV 1; linear; genomic DNA; STD; PRO; 7477 BP. XX AC J01636; J01637; K01483; K01793; XX DT 30-NOV-1990 (Rel. 26, Created) DT 09-SEP-2004 (Rel. 81, Last updated, Version 8) XX DE E.coli lactose operon with lacI, lacZ, lacY and lacA genes. XX KW acetyltransferase; beta-D-galactosidase; galactosidase; lac operon; KW lac repressor protein; lacA gene; lacI gene; lactose permease; lacY gene; KW lacZ gene; mutagenesis; palindrome; promoter region; KW thiogalactoside acetyltransferase. XX OS Escherichia coli OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; OC Enterobacteriaceae; Escherichia. XX RN [1] RP 1243-1266 RX DOI; 10.1073/pnas.70.12.3581. RX PUBMED; 4587255. RA Gilbert W., Maxam A.; RT "The nucleotide sequence of the lac operator"; RL Proc. Natl. Acad. Sci. U.S.A. 70(12):3581-3584(1973). XX RN [2] RP 1246-1308 RX DOI; 10.1073/pnas.70.12.3585. RX PUBMED; 4587256. RA Maizels N.M.; RT "The nucleotide sequence of the lactose messenger ribonucleic acid RT transcribed from the UV5 promoter mutant of Escherichia coli"; RL Proc. Natl. Acad. Sci. U.S.A. 70(12):3585-3589(1973). XX RN [3] RX PUBMED; 4598642. RA Gilbert W., Maizels N., Maxam A.; RT "Sequences of controlling regions of the lactose operon"; RL Cold Spring Harb. Symp. Quant. Biol. 38:845-855(1974). XX RN [4] RA Gilbert W., Gralla J., Majors A.J., Maxam A.; RT "Lactose operator sequences and the action of lac repressor"; RL (in) Sund H., Blauer G. (Eds.); RL PROTEIN-LIGAND INTERACTIONS:193-207; RL Walter de Gruyter, New York (1975) XX RN [5] RP 1146-1282 [Part of this file has been deleted for brevity] cgatttggct acatgacatc aaccatatca gcaaaagtga tacgggtatt atttttgccg 4560 ctatttctct gttctcgcta ttattccaac cgctgtttgg tctgctttct gacaaactcg 4620 ggctgcgcaa atacctgctg tggattatta ccggcatgtt agtgatgttt gcgccgttct 4680 ttatttttat cttcgggcca ctgttacaat acaacatttt agtaggatcg attgttggtg 4740 gtatttatct aggcttttgt tttaacgccg gtgcgccagc agtagaggca tttattgaga 4800 aagtcagccg tcgcagtaat ttcgaatttg gtcgcgcgcg gatgtttggc tgtgttggct 4860 gggcgctgtg tgcctcgatt gtcggcatca tgttcaccat caataatcag tttgttttct 4920 ggctgggctc tggctgtgca ctcatcctcg ccgttttact ctttttcgcc aaaacggatg 4980 cgccctcttc tgccacggtt gccaatgcgg taggtgccaa ccattcggca tttagcctta 5040 agctggcact ggaactgttc agacagccaa aactgtggtt tttgtcactg tatgttattg 5100 gcgtttcctg cacctacgat gtttttgacc aacagtttgc taatttcttt acttcgttct 5160 ttgctaccgg tgaacagggt acgcgggtat ttggctacgt aacgacaatg ggcgaattac 5220 ttaacgcctc gattatgttc tttgcgccac tgatcattaa tcgcatcggt gggaaaaacg 5280 ccctgctgct ggctggcact attatgtctg tacgtattat tggctcatcg ttcgccacct 5340 cagcgctgga agtggttatt ctgaaaacgc tgcatatgtt tgaagtaccg ttcctgctgg 5400 tgggctgctt taaatatatt accagccagt ttgaagtgcg tttttcagcg acgatttatc 5460 tggtctgttt ctgcttcttt aagcaactgg cgatgatttt tatgtctgta ctggcgggca 5520 atatgtatga aagcatcggt ttccagggcg cttatctggt gctgggtctg gtggcgctgg 5580 gcttcacctt aatttccgtg ttcacgctta gcggccccgg cccgctttcc ctgctgcgtc 5640 gtcaggtgaa tgaagtcgct taagcaatca atgtcggatg cggcgcgacg cttatccgac 5700 caacatatca taacggagtg atcgcattga acatgccaat gaccgaaaga ataagagcag 5760 gcaagctatt taccgatatg tgcgaaggct taccggaaaa aagacttcgt gggaaaacgt 5820 taatgtatga gtttaatcac tcgcatccat cagaagttga aaaaagagaa agcctgatta 5880 aagaaatgtt tgccacggta ggggaaaacg cctgggtaga accgcctgtc tatttctctt 5940 acggttccaa catccatata ggccgcaatt tttatgcaaa tttcaattta accattgtcg 6000 atgactacac ggtaacaatc ggtgataacg tactgattgc acccaacgtt actctttccg 6060 ttacgggaca ccctgtacac catgaattga gaaaaaacgg cgagatgtac tcttttccga 6120 taacgattgg caataacgtc tggatcggaa gtcatgtggt tattaatcca ggcgtcacca 6180 tcggggataa ttctgttatt ggcgcgggta gtatcgtcac aaaagacatt ccaccaaacg 6240 tcgtggcggc tggcgttcct tgtcgggtta ttcgcgaaat aaacgaccgg gataagcact 6300 attatttcaa agattataaa gttgaatcgt cagtttaaat tataaaaatt gcctgatacg 6360 ctgcgcttat caggcctaca agttcagcga tctacattag ccgcatccgg catgaacaaa 6420 gcgcaggaac aagcgtcgca tcatgcctct ttgacccaca gctgcggaaa acgtactggt 6480 gcaaaacgca gggttatgat catcagccca acgacgcaca gcgcatgaaa tgcccagtcc 6540 atcaggtaat tgccgctgat actacgcagc acgccagaaa accacggggc aagcccggcg 6600 atgataaaac cgattccctg cataaacgcc accagcttgc cagcaatagc cggttgcaca 6660 gagtgatcga gcgccagcag caaacagagc ggaaacgcgc cgcccagacc taacccacac 6720 accatcgccc acaataccgg caattgcatc ggcagccaga taaagccgca gaaccccacc 6780 agttgtaaca ccagcgccag cattaacagt ttgcgccgat cctgatggcg agccatagca 6840 ggcatcagca aagctcctgc ggcttgccca agcgtcatca atgccagtaa ggaaccgctg 6900 tactgcgcgc tggcaccaat ctcaatatag aaagcgggta accaggcaat caggctggcg 6960 taaccgccgt taatcagacc gaagtaaaca cccagcgtcc acgcgcgggg agtgaatacc 7020 acgcgaaccg gagtggttgt tgtcttgtgg gaagaggcga cctcgcgggc gctttgccac 7080 caccaggcaa agagcgcaac aacggcaggc agcgccacca ggcgagtgtt tgataccagg 7140 tttcgctatg ttgaactaac cagggcgtta tggcggcacc aagcccaccg ccgcccatca 7200 gagccgcgga ccacagcccc atcaccagtg gcgtgcgctg ctgaaaccgc cgtttaatca 7260 ccgaagcatc accgcctgaa tgatgccgat ccccacccca ccaagcagtg cgctgctaag 7320 cagcagcgca ctttgcgggt aaagctcacg catcaatgca ccgacggcaa tcagcaacag 7380 actgatggcg acactgcgac gttcgctgac atgctgatga agccagcttc cggccagcgc 7440 cagcccgccc atggtaacca ccggcagagc ggtcgac 7477 // You can specify a file of ranges to display in uppercase by giving the '-uppercase' qualifier the value '@' followed by the name of the file containing the ranges. (eg: '-upper @myfile'). The format of the range file is: * Comment lines start with '#' in the first column. * Comment lines and blank lines are ignored. * The line may start with white-space. * There are two positive (integer) numbers per line separated by one or more space or TAB characters. * The second number must be greater or equal to the first number. * There can be optional text after the two numbers to annotate the line. * White-space before or after the text is removed. An example range file is: # this is my set of ranges 12 23 4 5 this is like 12-23, but smaller 67 10348 interesting region You can specify a file of ranges to highlight in a different colour when outputting in HTML format (using the '-html' qualifier) by giving the '-highlight' qualifier the value '@' followed by the name of the file containing the ranges. (eg: '-highlight @myfile'). The format of this file is very similar to the format of the above uppercase range file, except that the text after the start and end positions is used as the HTML colour name. This colour name is used 'as is' when specifying the colour in HTML in a '' construct, (where 'xxx' is the name of the colour). The standard names of HTML font colours are given in: http://http://www.w3.org/TR/REC-html40/types.html#h-6.5 An example highlight range file is: __________________________________________________________________ # this is my set of ranges 12 23 red 4 5 darkturquoise 67 10348 #FFE4E1 __________________________________________________________________ Output file format Output files for usage example File: j01636.remap J01636 E.coli lactose operon with lacI, lacZ, lacY and lacA genes. BssKI TaqI AciI Ksp632I \ \ \ gacaccatcgaatggcgcaaaacctttcgcggtatggcatgatagcgcccggaagagagt 10 20 30 40 50 60 ----:----|----:----|----:----|----:----|----:----|----:----| ctgtggtagcttaccgcgttttggaaagcgccataccgtactatcgcgggccttctctca / / / / TaqI AciI | BssKI Ksp632I # Enzymes that cut Frequency Isoschizomers AciI 1 BssKI 1 Ksp632I 1 Bsu6I TaqI 1 # Enzymes which cut less frequently than the MINCUTS criterion # Enzymes < MINCUTS Frequency Isoschizomers # Enzymes which cut more frequently than the MAXCUTS criterion # Enzymes > MAXCUTS Frequency Isoschizomers # Enzymes that do not cut # No. of cutting enzymes which do not match the # SITELEN, BLUNT, STICKY, COMMERCIAL, AMBIGUOUS criteria 0 Output files for usage example 2 File: j01636.remap J01636 E.coli lactose operon with lacI, lacZ, lacY and lacA genes. Hin6I TaqI | HhaI | BsiYI | BssKI | | Hin6I | Ksp632I | | | HhaI AciI | | HpaII \ \ \ \ \ \ \ \ gacaccatcgaatggcgcaaaacctttcgcggtatggcatgatagcgcccggaagagagt 10 20 30 40 50 60 ----:----|----:----|----:----|----:----|----:----|----:----| ctgtggtagcttaccgcgttttggaaagcgccataccgtactatcgcgggccttctctca / / / / / / / /// | TaqI | Hin6I AciI | | ||BssKI BsiYI HhaI | | |HpaII | | Ksp632I | Hin6I HhaI # Enzymes that cut Frequency Isoschizomers AciI 1 BsiYI 1 Bsc4I BssKI 1 HhaI 2 Hin6I 2 HinP1I,HspAI HpaII 1 BsiSI Ksp632I 1 Bsu6I TaqI 1 # Enzymes which cut less frequently than the MINCUTS criterion # Enzymes < MINCUTS Frequency Isoschizomers # Enzymes which cut more frequently than the MAXCUTS criterion # Enzymes > MAXCUTS Frequency Isoschizomers # Enzymes that do not cut AclI BamHI BceAI BseYI BsrI ClaI EcoRI EcoRII HaeIII Hin4I HindII HindIII KpnI MaeII NotI # No. of cutting enzymes which do not match the # SITELEN, BLUNT, STICKY, COMMERCIAL, AMBIGUOUS criteria 0 Output files for usage example 3 File: j01636.remap J01636 E.coli lactose operon with lacI, lacZ, lacY and lacA genes. HspAI Hin6I TaqI HinP1I | BsiYI | HhaI | Bsc4I | Bsu6I | | HspAI | BssKI | | Hin6I | Ksp632I | | HinP1I | | HpaII | | | HhaI AciI | | BsiSI \ \ \ \ \ \ \ \ gacaccatcgaatggcgcaaaacctttcgcggtatggcatgatagcgcccggaagagagt 10 20 30 40 50 60 ----:----|----:----|----:----|----:----|----:----|----:----| ctgtggtagcttaccgcgttttggaaagcgccataccgtactatcgcgggccttctctca / / / / / / / /// | TaqI | HinP1I AciI | | ||BssKI Bsc4I | Hin6I | | |BsiSI BsiYI | HspAI | | |HpaII HhaI | | Ksp632I | | Bsu6I | HinP1I | Hin6I | HspAI HhaI # Enzymes that cut Frequency AciI 1 Bsc4I 1 BsiSI 1 BsiYI 1 BssKI 1 Bsu6I 1 HhaI 2 Hin6I 2 HinP1I 2 HpaII 1 HspAI 2 Ksp632I 1 TaqI 1 # Enzymes which cut less frequently than the MINCUTS criterion # Enzymes < MINCUTS Frequency # Enzymes which cut more frequently than the MAXCUTS criterion # Enzymes > MAXCUTS Frequency # Enzymes that do not cut AclI BamHI BceAI Bse1I BseYI BshI BsrI ClaI EcoRI EcoRII HaeIII Hin4I HindII HindIII HpyCH4IV KpnI MaeII NotI # No. of cutting enzymes which do not match the # SITELEN, BLUNT, STICKY, COMMERCIAL, AMBIGUOUS criteria 0 Output files for usage example 4 File: j01636.remap J01636 E.coli lactose operon with lacI, lacZ, lacY and lacA genes. Ksp632I >.........==== HpaII >=== HhaI BssKI ==>= >===== TaqI Hin6I HhaI >=== >=== ==>= BsiYI AciI Hin6I ======>==== >..==== >=== gacaccatcgaatggcgcaaaacctttcgcggtatggcatgatagcgcccggaagagagt 10 20 30 40 50 60 ----:----|----:----|----:----|----:----|----:----|----:----| ctgtggtagcttaccgcgttttggaaagcgccataccgtactatcgcgggccttctctca ====<====== <=== ===< BsiYI AciI Hin6I ===< ===< =<== <.....==== TaqI Hin6I HhaI Ksp632I =<== =====< HhaI BssKI ===< HpaII # Enzymes that cut Frequency Isoschizomers AciI 1 BsiYI 1 Bsc4I BssKI 1 HhaI 2 Hin6I 2 HinP1I,HspAI HpaII 1 BsiSI Ksp632I 1 Bsu6I TaqI 1 # Enzymes which cut less frequently than the MINCUTS criterion # Enzymes < MINCUTS Frequency Isoschizomers # Enzymes which cut more frequently than the MAXCUTS criterion # Enzymes > MAXCUTS Frequency Isoschizomers # Enzymes that do not cut AclI BamHI BceAI BseYI BsrI ClaI EcoRI EcoRII HaeIII Hin4I HindII HindIII KpnI MaeII NotI # No. of cutting enzymes which do not match the # SITELEN, BLUNT, STICKY, COMMERCIAL, AMBIGUOUS criteria 0 The name of the sequence is displayed, followed by the description of the sequence. The formatted display of cut sites on the sequence follows, with the six-frame translation below it. The cut sites are indicated by a slash character '\' that points to the poition between the nucleotides where the cuts occur. Cuts by many enzymes at the same position are indicated by stacking the enzyme names on top of each other. At the end the section header 'Enzymes that cut' is displayed followed by a list of the enzymes that cut the specified sequence and the number of times that they cut. For each enzyme that cuts, a list of isoschizomers of that enzyme (sharing the same recognition site pattern and cut sites) is given. This is followed by lists of the enzymes that do cut, but which cut less often than the '-mincut' qualifier or more often than the '-maxcut' qualifier. Any of the isoschizomers that are excluded from cutting, (either through restrictions such as the permitted number of cuts, blunt cutters only, single cutters only etc. or because their name has not been given in the input list of enzymes), will not be listed. Then a list is displayed of the enzymes whose names were input and which match the other criteria ('-sitelen', '-blunt', '-sticky', '-ambiguity' or '-commercial') but which do not cut. Finally the number of enzymes that were rejected from consideration because they do not match the '-sitelen', '-blunt', '-sticky', '-ambiguity' or '-commercial' criteria is displayed. The '-flatreformat' qualifier changes the display to emphasise the recognition site of the restriction enzyme, which is indicated by a row of '=' characters. The cut site if pointed to by a '>' or '<' character and if the cut site is not within or imemdiately adjacent to the recognition site, they are linked by a row of '.' characters. The name of the enzyme is displayed above (or below when the reverse sense site if displayed) the recognition site. The name of the enzyme is also displayed above the cut site if this occurs on a different display line to the recognition site (i.e. if it wraps onto the next line of sequence). Data files EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA. To see the available EMBOSS data files, run: % embossdata -showall To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run: % embossdata -fetch -file Exxx.dat Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata". The directories are searched in the following order: * . (your current directory) * .embossdata (under your current directory) * ~/ (your home directory) * ~/.embossdata The EMBOSS REBASE restriction enzyme data files are stored in directory 'data/REBASE/*' under the EMBOSS installation directory. These files must first be set up using the program 'rebaseextract'. Running 'rebaseextract' may be the job of your system manager. The data files are stored in the REBASE directory of the standard EMBOSS data directory. The names are: * embossre.enz Cleavage information * embossre.ref Reference/methylation information * embossre.sup Supplier information The column information is described at the top of the data files The reported enzyme from any one group of isoschizomers (the prototype) is specified in the REBASE database and the information is held in the data file 'embossre.equ'. You may edit this file to set your own preferred prototype, if you wish. The format of the file "embossre.equ" is Enzyme-name Prototype-name i.e. two columns of enzyme names separated by a space. The first name of the pair of enzymes is the name that is not preferred and the second is the preferred (prototype) name. Notes The Restriction Enzyme database (REBASE) is a collection of information about restriction enzymes and related proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits and control proteins are also included. Most recently, putative DNA methyltransferases and restriction enzymes, as predicted from analysis of genomic sequences, are also listed. The home page of REBASE is: http://rebase.neb.com/ Where the translation is given in the output file, the genetic code and one or more frames for translation may be specified. The -no[reverse] option specifies whether the translation (and cut and recognition sites) are shown for the reverse sense strand. By default, only one enzyme of any group of isoschizomers (enzymes that have the same recognition site and cut positions) is reported. This behaviour can be changed by specifying -nolimit, in which case all isoschizomers are reported. The default behaviour uses the representative enzyme of an isoschizomer group (the prototype) which is specified in the EMBOSS data file embossre.equ. This file is generated from the REBASE database by running rebaseextract. You may edit this file to set your own preferred prototype, if you wish. As well as the display of where enzymes cut in the sequence, remap displays: * The list of enzymes that cut the sequence and match the required criteria. * The list of enzymes that cut the sequence and fail the MINCUTS criteria. * The list of enzymes that cut the sequence and fail the MAXCUTS criteria. * The list of enzymes that do not cut the sequence but which match all the required criteria. * The number of enzymes that cut the sequence and fail the SITELEN, BLUNT, STICKY, COMMERCIAL, AMBIGUOUS criteria. References None. Warnings remap uses the EMBOSS REBASE restriction enzyme data files stored in directory data/REBASE/* under the EMBOSS installation directory. These files must first be set up using the program rebaseextract. Running rebaseextract may be the job of your system manager. Diagnostic Error Messages None. Exit status It always exits with status 0. Known bugs None. See also Program name Description abiview Display the trace in an ABI sequencer file backtranambig Back-translate a protein sequence to ambiguous nucleotide sequence backtranseq Back-translate a protein sequence to a nucleotide sequence checktrans Reports STOP codons and ORF statistics of a protein cirdna Draws circular maps of DNA constructs coderet Extract CDS, mRNA and translations from feature tables iep Calculate the isoelectric point of proteins lindna Draws linear maps of DNA constructs pepinfo Plot amino acid properties of a protein sequence in parallel pepnet Draw a helical net for a protein sequence pepwheel Draw a helical wheel diagram for a protein sequence plotorf Plot potential open reading frames in a nucleotide sequence prettyplot Draw a sequence alignment with pretty formatting prettyseq Write a nucleotide sequence and its translation to file recoder Find restriction sites to remove (mutate) with no translation change redata Retrieve information from REBASE restriction enzyme database restover Find restriction enzymes producing a specific overhang restrict Report restriction enzyme cleavage sites in a nucleotide sequence showfeat Display features of a sequence in pretty format showorf Display a nucleotide sequence and translation in pretty format showpep Displays protein sequences with features in pretty format showseq Displays sequences with features in pretty format silent Find restriction sites to insert (mutate) with no translation change sixpack Display a DNA sequence with 6-frame translation and ORFs transeq Translate nucleic acid sequences Author(s) Gary Williams formerly at: MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Written Spring 2000 Changed 7 Dec 2000 - GWW - to declare isoschizomers that cut Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None