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.
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.
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:
Please report bugs or other problems here:
1.3 — Added directory listing
1.2 — Added Visual Enzyme Match Matrix
1.1 — Added Taxonomic Rank Checker
1.0 — Initial Release
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)