REHUNT (Restriction Enzymes HUNTing)

REHUNT v1.21

REHUNT (Restriction Enzymes HUNTing) v1.21 is released on April 11, 2018.

This is stable version.

It is a free and open source package implemented in JAVA for

providing many useful methods for biological sequence analysis

(especially in SNP genotyping) around restriction enzymes.

Requirements

• JAVA Runtime Environment (JRE) 8 or later.
  • If you can not run REHUNT or you are getting an error message, please download and install the laster JRE from:
    • http://www.oracle.com/technetwork/java/javase/downloads/index.html

Database

REBASE download fromhttp://rebase.neb.com/rebase/rebase.files.html

at 11. All Enzymes (parsed references) file.

The current REBASE version is 709: parsrefs.709

update: Aug 28 2017

Source Code

Full source code for REHUNT is available at:

Yu-Huei Cheng website: https://sites.google.com/site/yhcheng1981/rehunt

SourceForge: https://sourceforge.net/projects/rehunt/

GitHub: https://github.com/yuhuei/rehunt

LICENSE

REHUNT is implemented and maintained by Yu-Huei Cheng from 2007 to 2018. REHUNT is published under GPLv3 license, please see the LICENSE file.

All academic researchers are encouraged to use it to apply to their studies or integrate it into their systems and applications.

Non-academic users or commercial needs are also welcome to use it.

For further information or additional applications welcome to contact with the author Yu-Huei Cheng <yuhuei.cheng@gmail.com>.

Author

Yu-Huei Cheng

Email: yuhuei.cheng@gmail.com

Web: https://sites.google.com/site/yhcheng1981/

REHUNT Updated Log

• 2017/10/15 by Yu-Huei Cheng:

REHUNT v1.2 is released.

• 2017/10/14 by Yu-Huei Cheng:

1. Update examples and improve codes to relase REHUNT v1.2.

2. The document for REHUNT v1.2 is now available.

3. Update REBASE to version 709 with the latest update on Aug 28 2017.

• 2017/02/04 by Yu-Huei Cheng:

Update REBASE to version 702 with the latest update on Jan 29 2017.

• 2016/10/06 by Yu-Huei Cheng:

1. The REHUNT has been successfully applied to natural PCR-RFLP primer design for SNP genotyping. The publication is available at: http://ieeexplore.ieee.org/document/7530862/.

• 2016/10/05 by Yu-Huei Cheng:

1. Update examples and improve codes to relase REHUNT v1.1.

2. The document for REHUNT v1.1 is now available.

• 2016/09/28 by Yu-Huei Cheng:

Update REBASE to version 609 with the latest update on Aug 29 2016.

• 2014/04/24 by Yu-Huei Cheng:

Update REBASE to version 307 with the latest update on Mar 31 2014.

• 2014/03/01 by Yu-Huei Cheng:

Update REBASE to version 402 with the latest update on Jan 30 2014.

• 2013/07/06 by Yu-Huei Cheng:

Update REBASE to version 307 with the latest update on Jun 30 2013.

• 2012/07/29 by Yu-Huei Cheng:

Construct the REHUNT version 1.0 API documents.

• 2012/07/28 by Yu-Huei Cheng:

Construct the project in Google code for releasing REHUNT version 1.0.

• 2012/07/27 by Yu-Huei Cheng:

1. Modified the bugs for the judgement of specific restriction enzymes, and remove setSpecificEnzyme(boolean isSpecificEnzyme) method in RFLP.java.

2. Add regionMatchCount(String seq, String subSeq) method in RFLPprocess.java for counting the repeat number of subSeq in seq.

3. Make the examples for accessible.

• 2012/07/26 by Yu-Huei Cheng:

1. Clear the content of enzymeNameList and cutEnzymesList before the isCanCut and isCanCut_dNTPs methods in JudgeRFLP.java are performed.

2. Modified setSpecificityEnzyme(ifSpecificityEnzyme) method as setSpecificityEnzyme(isSpecificEnzyme) through all source documents.

• 2012/07/25 by Yu-Huei Cheng:

Named the package as REHUNT, and modified the all annotations for the source codes.

• 2011/11/09 by Yu-Huei Cheng:

1. Delete REBASE_RelatedSeq.java and merge its methods to REBASE.java.

2. Add and modify annotations for the source codes of REHUNT.

• 2010/05/07 by Yu-Huei Cheng:

1. Take off the function of flanking 20 bp to analyze RFLP for identifing the specific restriction enzymes.

2. The filed ifSpecificityEnzyme is problematic and ifSpecificityEnzyme must be set to false for correctness in current version.

• 2009/09/03 by Yu-Huei Cheng:

Reserve getPosMultiSeq_dNTPs method in SeqProcess.java.

• 2009/08/24 by Yu-Huei Cheng:

1. Update isCanCut and isCanCut_dNTPs methods in JudgeRFLP.java use flanking 20 bp to analyze RFLP for the performance.

2. Modified getPosMultiSeq_dNTPs method in SeqProcess.java.

• 2009/08/06 by Yu-Huei Cheng:

1. Set the default isIUPACenzyme as true and isSpecificityEnzyme as false in JudgeRFLPBatchThread.java.

2. The variation sequence uses flanking 20 bp to analyze RFLP.

• 2009/06/30 by Yu-Huei Cheng:

Update REBASE to version 906.

• 2009/02/03 by Yu-Huei Cheng:

Update REBASE to version 902.

• 2009/02/02 by Yu-Huei Cheng:

1. Add haveSpecificityMatches method to RFLPprocess.java for judging the specificity of restriction enzymes.

2. Add the field ifSpecificityEnzyme to RFLP.java, JudgeRFLP.java and Example.java to applied to the haveSpecificityMatches method.

3. Add the functions for setting IUPAC and Specific restriction enzymes in JudgeRFLP.java.

• 2008/07/10 by Yu-Huei Cheng:

Add JudgeRFLPBatchThread.java to analyze multiple sequences for RFLP.