Upcoming Events

July 19-23, 2013: 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB).

April 7-10, 2013: 17th Annual International Conference on Research in Computational Molecular Biology (RECOMB).

April 15-19, 2013: IEEE Symposium on Computational Intelligence in Bioinformatics & Computational Biology.

March 4-6, 2013: 5th international conference on Bioinformatics & Computational Biology (BICoB).

More events....



News     

Oct 18, 2012: A new Postdoctoral Fellow, Dr. Sitanshu Sekhar Sahu has joined our lab.

Aug 13-17, 2012: A comprehensive 1-week Bioinformatics Workshop was organized on campus; co-organized by OSU's iCREST center. Visit facebook page for details.

Apr 23, 2012: Co-hosted Dr. James Tiedje (Director, NSF Center for Microbial Ecology, Michigan State University) as an invited iCREST speaker; see flyer for details.

Apr 13, 2012: World renowned Computational Biologist, Dr. Eugene Koonin (NCBI) visited our lab, and delivered an invited lecture on campus as part of iCREST speaker series; see flyer for details. Video on YouTube.

Mar 16, 2012: We welcome Dr. Chris Town (Group leader, Plant Genomics, JCVI) as an invited iCREST speaker; see flyer for details.

Feb 14, 2012: KBL receives new grant from OCAST to develop bioinformatics systems for plant-microbe interaction networks; immediate Postdoc opening available.

Oct 21, 2011: We welcome Dr. Patrick X. Zhao (Head, Bioinformatics Lab, Noble Foundation) as an invited iCREST speaker; see flyer for details.

Sep 17, 2011: Tyler Weirick joins our lab (under iCREST) as a Graduate Research Assistant.

Aug 17, 2011: Robyn Kelley, a new master's student joins our lab as a Graduate Research Assistant.

July 21, 2011: KBL receives OSU funding to establish an iCREST center for Bioinformatics and Computational Biology.

June 08, 2011: KBL welcomes its first student, Kalpana Varala to work as a summer scholar in lab.



 




ligpred
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Welcome to LigPred

Lignin is the second most abundant organic polymer on earth. Found as a major component of plant cell walls and some algae this complex homopolymer contains a higher energy density than cellulose. Thus it is no surprise many industrial applications involving lignin have developed such as the ability to derive useful chemicals from lignin or uses based on its structural properties. These structural properties mainly it's recalcitrance continue to be an issue for the use of many kinds of plant material for biofuels and livestock food efficiency. Research has looked to plants to reduce the recalcitrance and quantity of lignin produced by plants and to lignin degraders for more efficient enzymes as solutions to reducing the negative impact of lignin in biofuel production. Next-generation sequencing offers a powerful tool for the study of the genetics of lignin synthesis and degradation though the study of plant genomes and metagenomes of lignin degrading environments. However, many proteins function cannot be accurately predicted with general identification techniques such as sequence similarity, clustering, motifs, or evolutionary relationships.

LigPred is an attempt to discover novel lignin related proteins not discoverable through more general means. To accomplish this we created high quality training sets from known lignin related enzymes and created models using a support vector machine (SVM). This allows for greater ability to recognize certain types of proteins at the expense of the inability to generally classify proteins.

We offer a web tool which accepts fasta data and will attempt to classify the sequences as belonging to lignin related enzyme class or not. In the event there is no relation the out will simply return unknown.

based method for recognition of enzymes related to degradation and synthesis of lignin. It can predict the 37 different classes of lignin related enzymes. See the table below for classes. The primary motivation for its development is to search genomic and metagenomic data for lignin related enzymes with low sequence similarity to currently known lignin related enzymes.

LigPred is made possible by generous funding from Oklahoma State University Provost through the iCREST research group and OCAST.


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