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February 2014 Vntrseek version 1.05 is now available for download here.

November 2012 New TRF version 4.07b is now available for download here.

March 2007 IRF commandline version is now available for download here.

February 2007 TRDB version 2.2 has some important features regarding downloads and reports, please check the about pages for more information regarding this release.

January 2007 Denise Mak presented the following paper at the APBC 2007 conference in Hon Kong: All hits all the time: parameter free calculation of seed sensitivity, Denise Y.F. Mak, Gary Benson

December 2006 The following paper was published: TRDB - The Tandem Repeats Database, Nucleic Acids Research, 2006, Vol. 00, Database issue D1-D8 doi:10.1093/nar/gkl1013

March 2006 Added a button to TRDB/IRDB to quickly check a repeat against the Repeat Masker database.

January 2006 January 2006 Added Search for Exact Pattern tool To TRDB/IRDB which uses an efficent aho-corasick algorithm to search through many patterns at the same time.

December 2005 December 2005 Added Set Import tool to TRDB/IRDB .

October 2005 October 2005 TRF 4.0 is now availiable for download.

Septemeber 2005 Septemeber 2005 We processed a number of genomes for TRDB with standard 2,7,7,50 parameters. Theses can be viewed using a guest account. To find smaller and more degenerated tandem repeats we also processed a batch under 2,5,5,20. The later results are only available as text files here.

August 2005 August 2005 Added a new clustering method to TRDB, which utilizes the Partition Around Medoids method described in our recent paper.

June 2005 June 2005 Published a paper called Evaluating distance functions for clustering tandem repeats; Suyog Rao, Alfredo Rodriguez and G. Benson.

December 2004 Added Set Comparison tool (TRDB only so far) to compare two sets ran at different parameters or with a different algorithm version. Another tool we added to TRDB is the sub-pattern detection tool that tests repeats for possible sub-patterns.

November 2004 We published a paper on large inverted repeats we found in the human genome in the Genome Research magazine: INVERTED REPEAT STRUCTURE OF THE HUMAN GENOME Peter E. Warburton, Joti Giordano, Fanny Cheung, Yevgeniy Gelfand and Gary Benson.

July 2004 Added a lot of IRF modifications like searching for mirror repeats, GT match (both detection and alignment) and other things.

February 2004 We are getting a lot more computer power. 3 New nodes are about to be added to our cluster, which will bring it to a total of 7 high performance machines. Also, we are in the process of increasing the server disk space. After completion, our server will quadruple the storage space.

January 2004 We made some of our code open source. A CGI library, a GU library (tutorial) for creating graph plots on the fly (it uses freely distributed gdlib for drawing and allows creating PNG and JPEG line plots, bar graphs and scatter plots). Code is available for download on CodeHub, which is another new addition. CodeHub is a repository of code written by LBI employees and students. Click here to go to the download page. Finally, the last of our tools, the "Mutation Master" has been moved to our new server. New versions of TRDB/IRDB (2.14) are now available which have improved distribution and scatter plots(also new) and new multiple set merge functions. A lot of little fixes on the IRF tool.

December 2003 Computational cluster is up and running. TRF and IRF sequence processing are now done on the cluster. We expect this to reduce the time it takes to analyze sequences as well as improving the interactivity of TRDB and IRDB. Plans are under way to move other computationally intensive operations into the cluster.

October 2003 Composition Alignment, or scrambled alignment, is a new kind of alignment which avoids the overdependence of other alignment methods on position-by-position matching. It was first presented by Dr. Benson in Budapest, Hungary on September 2003. We have provided code for download and a web interface available from our tools menu.

Septemeber 2003 Our lab has moved! We are now located in Boston University. We have a backup machine serving pages back in Mount Sinai while we are setting up here. Our next big project will be a cluster for the Tandem Repeats database which has significantly grown since we first launched it a year ago. We already bought the UPS emergency power backup system and plugged our server into it.

February 2003 We finally automated the process of annotating sequences in our databases by writing a program that connects to various DAS (distributed annotations server) servers and updates annotations once a week. IRDB/TRDB 2.01 is now officially complete, frozen, and work on the next version is already in progress.

January 2003 A new tool is now avalible for calculating RNA folding structures called RNA Fold Support. We added the reports feature to TRDB/IRDB Version 2.01. Many bugs fixed, not so many introcuded :)

December 2002 More work on IRF. Were able to speed it up significantly by the profiler to find areas of inefficient code. Added a new feature to it to ignore masked out N/lowercase letters during the alignment (very useful in some cases when the sequence is masked.) The only thing to do is to iron out a few bugs and add some output options and redundancy control. Added a new feature to TRDB multiple alignment to have it automatically pick out the best alignment order.

November 2002 We merged two of our web databases TRDB and IRDB. Because we determined that they share about 70% of code, a reusable library was produced that is used by both of them. We also decided that it's in our best interests to have them share some of the data (like users and their sequences and annotations.) So when the user is registered for one database, he can automatically use the other one (assuming his name is on the pre approved list in both of them. Preapproved list is a temporary feature we have in place because we are still officially in testing phase and want to limit our users for now. ) New reusable source and data are now part of the reusable package LBI web core which we plan to extensively develop over the years and use for many other projects.

October 2002 Thanx to our graduate students Sarah Nahmias and Patrick Coskren we finally annotated both Human and C. elegans genomes in TRDB. Human annotations took a lot of time because the files had to be significantly rewamped to extract UTR data. More detail in TRDB help. The memory problem with alignment of long repeats in TRDB is finally fixed so we finally could process the whole Human genome (which we did.) Added the distribution viewer for IRF web interface.

September 2002 This site is created. For a long time we needed a page that would serve as the research center and provide links to the various tools we have available. Finally, we've put together these pages.

August 2002 The preliminary work on IRF is almost complete. Finding some bugs took a long time. We have a working version, but we need to add a lot of statistical analysis to speed it up.

Version 1.01 of TRDB has been installed on the new server. The installation when relatively smooth but we encountered a few problems with the instructions. We have updated the installation manual accordingly.

June 2002 We received the new machine to replace the old server. It's a Dell PowerEdge 4600 with 2 1.8 Xeon processors. This machine employs hyper-threading technology (2 context switch free threads per processor) so we effectively have 4 processors. We have set it up and are slowly moving our stuff to it.

 

  Quick Links:

Composition Alignment: download | web | sim
TRDB | IRDB
TRF : download | web
IRF : download
FHub | CHub
K'nex DNA Models

  Latest News:

New Vntrseek 1.05 version is now available for download.
New TRF 4.07b version is now available for download.
IRF command line version is now available for download.

  Page last updated:11/29/12