restover

restover

restover takes a specified sequence and a short sequence of a cut-site overhang and searches the REBASE database for matching enzymes that create the desired overhang sequence when they cut the input sequence.

Here is a sample session with restover:

% restover Finds restriction enzymes that produce a specific overhang Input sequence(s): em:hsfau Overlap sequence: cg Output file [hsfau.restover]:

Mandatory qualifiers:

[-sequence] (seqall)

Sequence database USA.

[-seqcomp] (string)

Overlap sequence.

[-outfile] (outfile)

Output filename.

Advanced qualifiers:

-min (integer)

Minimum cuts per restriction enzyme.

-max (integer)

Maximum cuts per restriction enzyme.

-single (boolean)

Force single site only cuts

-threeprime (boolean)

3' overhang? (else 5') e.g., BamHI has CTAG as a 5' overhang, and ApaI has CCGG as 3' overhang.

-[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.

-html (boolean)

Create HTML output.

-[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

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