restrict

restrict

restrict uses the REBASE database of restriction enzymes to predict cut sites in a DNA sequence.

Here is a sample session with restrict:

% restrict Finds restriction enzyme cleavage sites Input sequence(s): embl:hsfau Minimum recognition site length [4]: Comma separated enzyme list [all]: Output file [hsfau.restrict]:

Mandatory qualifiers:

[-sequence] (seqall)

Sequence database USA.

-sitelen (integer)

Minimum recognition site length.

-enzymes (string)

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
[-outfile] (report)

Output report filename.

Advanced qualifiers:

-min (integer)

Minimum cuts per restriction enzyme.

-max (integer)

Maximum cuts per restriction enzyme.

-single (boolean

Force single site only cuts.

-[no]blunt (boolean)

Allow blunt end cutters.

-[no]sticky (boolean)

Allow sticky end cutters.

-[no]ambiguity (boolean)

Allow ambiguous matches.

-plasmid (boolean)

Allow circular DNA.

-[no]commercial (boolean)

Only enzymes with suppliers.

-datafile (string)

Alternative restriction enzyme data file.

-[no]limit (boolean)

Limits reports to one isoschizomer.

-preferred (boolean)

Report preferred isoschizomers.

-alphabetic (boolean)

Sort output alphabetically.

-fragments (boolean)

Show fragment lengths.

-name (boolean)

Show sequence name.



Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

Similar book on Amazon

flylib.com © 2008-2017.
If you may any questions please contact us: flylib@qtcs.net