REMAP : Display a sequence with restriction cut sites, translation etc.. (EMBOSS)

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input Section

required Section

advanced Section

output Section

input Section

sequence -- DNA [sequences] (-sequence) : please enter either :

the name of a file:
or the actual data here:

(sequence format)

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required Section

Comma separated enzyme list (-enzymes)

Minimum recognition site length (-sitelen)

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advanced Section

Minimum cuts per RE (-mincuts)
Maximum cuts per RE (-maxcuts)
Force single site only cuts (-single)
Allow blunt end cutters (-blunt)
Allow sticky end cutters (-sticky)
Allow ambiguous matches (-ambiguity)
Allow circular DNA (-plasmid)
Only enzymes with suppliers (-commercial)

Code to use -- Genetic codes (-table)

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Output sequence details to a file (-outfile)
List the enzymes that cut (-cutlist)
Display RE sites in flat format (-flatreformat)
Limits reports to one isoschizomer (-limit)
Report preferred isoschizomers (-preferred)
Display translation (-translation)
Display cut sites and translation of reverse sense (-reverse)
Minimum size of ORFs (-orfminsize)
Regions to put in uppercase (eg: 4-57,78-94) (-uppercase)
Regions to colour in HTML (eg: 4-57 red 78-94 green) (-highlight)
Display protein sequences in three-letter code (-threeletter)
Number the sequences (-number)
Width of sequence to display (-width)
Line length of page (0 for indefinite) (-length)
Margin around sequence for numbering (-margin)
Display sequence ID (-name)
Display description (-description)
Offset to start numbering the sequence from (-offset)
Use HTML formatting (-html)

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Some explanations about the options

input Section
enter either the name of a file or the actual data: if you are using Netscape 2.x or later, you can select a file by typing its name, or better, by selecting it with the Netscape file browser (Browse button); OR you can type your data in the next area, or cut and paste it from another application.; (but not both)
required Section
Comma separated enzyme list (-enzymes): 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
output Section
Output sequence details to a file (-outfile): If you enter the name of a file here then this program will write the sequence details into that file.
Minimum size of ORFs (-orfminsize): Minimum size of Open Reading Frames (ORFs) to display in the translations.
Regions to put in uppercase (eg: 4-57,78-94) (-uppercase): 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
Regions to colour in HTML (eg: 4-57 red 78-94 green) (-highlight): 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 specifed as '@filename'.
Display sequence ID (-name): Set this to be false if you do not wish to display the ID name of the sequence
Display description (-description): Set this to be false if you do not wish to display the description of the sequence
Sequence format: The sequence will be automatically converted in the format needed for the program; providing you enter a sequence either:; in plain (raw) sequence format or in one of the following known formats:; IG,GenBank,NBRF,EMBL,GCG,DNAStrider,Fitch,fasta,Phylip,PIR,MSF,ASN,PAUP,CLUSTALW; You may enter in the text area a database entry code, or an accession number, in this form:
database:entry_name
or:
database:accession.

Pise form generator version: 5.a (16 Dec 2002 11:55)