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REPK

Restriction Enzyme Picker Online, v.1.2

by Gabrielle Rocap and Eric Collins (rec3141.at.gmail.com)

REPK (Restriction Endonuclease Picker) finds sets of 4 commercially available restriction endonucleases which together uniquely differentiate designated sequence groups from a supplied FASTA format sequence file for use in T-RFLP. If you have a database of known sequences from an environment, this program could be useful to pick some enzymes that uniquely discriminate the different groups in your database.

Read the Manual

Enter your FASTA aligned sequences here:
(Here is an example input file: alignment5.txt)

Select the enzymes you would like to use: (REBASE Version 907)
(Hold down the [Control] key to deselect, or to select multiple enzymes)
At least two enzymes must be used.
NEB list of isoschizomers, the first (alphabetically) is shown below.
Type IIA enzymes (forward and reverse [+])

Enter any custom enzymes you would like to use in the following format (where ^ is the cut site):
NoCut [tab] zzz^zzz

Taxonomic rank: : which taxonomic group do you want separated out?
CHECK TAXONOMIC RANKS INSTEAD OF RUNNING REPK

Cutoff: : furthest apart two fragments can be in length and still be considered the same fragments

Min Fragment Lengths: : shortest acceptable fragment (must be greater than Cutoff)

Max Fragment Lengths: : longest acceptable fragment

Stringency: : an enzyme must distinguish MORE than this percent of groups to be acceptable

Max Missing Group Combinations: : the number of missing groups allowed

Max Matches Returned: : the most number of matches to print out (maximum 1000)



OPTIONAL -- Enter your RDP Classifier output file here -- OPTIONAL
(Here is an example input file: rdpdownload5.txt or generate your own here: RDP-Classifier)



CITE REPK
If you find REPK useful in your research please cite:

Collins, R. E. and G. Rocap. 2007. REPK: an analytical web server to select restriction endonucleases for terminal restriction fragment length polymorphism analysis. Nucleic Acids Res. 35 (Database issue): W58-W62; doi:10.1093/nar/gkm384 [Free full text]

Source code, help, and license information is available via Google Code:
http://code.google.com/p/repk

Please report bugs or other problems here:
http://code.google.com/p/repk/issues/list

Version Changes
1.2 -- Added Visual Enzyme Match Matrix
1.1 -- Added Taxonomic Rank Checker
1.0 -- Initial Release

 

NSF logo

Support for the development of REPK provided by the National Science Foundation under Grant No. OPP-0327244 to J.W. Deming and OCE-0822026 and OCE-0352190 to G. Rocap, as well as a Washington Sea Grant award to J.W. Deming.

Any opinions, findings and conclusions or recomendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation (NSF)

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