REPK

Restriction Enzyme Picker Online, v.1.3

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. Please cite our manuscript in any publication making use of enzymes chosen with REPK.

Read the Manual
REPK may take HOURS when a lot of groups are used. See note below.

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

Select the enzymes you would like to use: (REBASE Version 207 )
(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

Group Subset Delimiter : the character used to separate groups in your FASTA sequence names -->

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 maximum number of matches to print out (max allowed 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)



NOTE: Some recent runs with more than 75 groups and 179 enzymes took 4 hours to complete. Dont close the page until it says "DONE". If you close the page then the results.html file will not update but the program will continue running. As of 26/01/2010 You can check for these files by browsing to the base directory of the REPK run, e.g. http://rocaplab.ocean.washington.edu/cgi-bin/repk/RESULTS/REPK_2010026-1323-32027e46281c7b3c/ where REPK_2010026-1323-32027e46281c7b3c is the unique run ID.

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
1.3 -- Added directory listing
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)