Publicly Available Software

Following is a list of software produced by this lab which is being made available for use by the genomics community.

1. ESTprep3.1.4 (released on January 10, 2003). This program is used to pre-process EST reads in a mixed-tissue library environment. The software is written in C and designed to run under the UNIX operating system. Only standard C and libraries are needed so this package should be able to run on most operating systems. ESTprep has been successfully used on Linux, Solaris, Windows (98, NT), and Mac OS X. You may view documentation regarding the context of the use of ESTprep in our lab.
   Installation and Documentation
   ESTprep3.1 (released on June 15, 2001).
   ESTprep1.1 (released on May 14, 1998).
   
   These files contain predetermined set of library tags for use with prep's double error detection and single error correction capabilities. The double error detection feature finds invalid library tag markers. The single error correction feature detects library tags containing one error and produces it valid counterpart.
   Set of 288 words, with dH = 5, dE = 3
   Set of 64 words, 4 subsets of 16 words
   Set of 27 words, fixed guard postition
   Set of 28 words, no fixed guard postion
   
   
2. RHScorer1.0(released on September 1, 1998). This tool is used to score gels...The software is written entirely in Java.It consists of client applet and a server.The server is used to maintain the Gel Images and scores. The applet is used to score the gels.
   The following documents will be useful for installation and using the software.
   Requirements and installation
   Server Information
   Client Applet Information



3. RHScorer2.0(released on Feb 10, 1999).The new installation document has the recent enhancements and on instructions on how to install the software.
   Requirements and installation



4. RHScorer2.1(released on Mar 10,1999).
   CHANGES from the version 2.0
   * Added the ability to load the previous scores if the gel is already scored. Refer the CHANGES file to use the new feature



5. tlcluster This program is used to perform clustering on fasta formatted sequences. The program is written in C and designed to run under the UNIX operating system. Only standard C and UNIX libraries are needed so this package should be able to run on almost any UNIX installation.
   tlhistogram complements tlcluster by providing some statistics that result from tlcluster. Written in C.
   documentation



6. Clustering @ CLCG
   uicluster2.1.1 This program is an updated version of tlcluster that is much faster and adds new features such as reverse complement checking. In addition to optimization and reverse checking, it performs an extended search of all primaries for each sequence being clustered. The program is written in C and designed to run under the UNIX operating system. Only standard C and UNIX libraries are needed so this package should be able to run on almost any UNIX installation.
   uicluster3.0.5 This is the latest version of uicluster, which improves on its predecessor by adding parallel execution capabilties. The parallelism is implemented using MPICH MPI library.
   



7. UITagCreator1.9(released on July 22th, 2002)
   UITagCreator is used for the creation of fixed-length pooled library tags for EST-Based Gene Discovery. The software is written in C and designed to run under the UNIX operating system. Only standard C and UNIX libraries are needed so this package should be able to run on almost any UNIX installation.
   Installation and Documentation
   This file contains a set of 288 tags currently in use at the University of Iowa. Each tag is Hamming distance 5 and edit distance 3 from all others.
   
8. Ace_splitter.jar(released on May, 2004)
   This is a java program that splits Ace files into separate files for each Contig.
   
9. blatService.jar(released on July, 2004)
   This jar has both a webservice as well as a sample client. It allows connection to a blat service over the web, as well as parsing the returned results and retrieving the genomic sequence
   blatServiceClient.pl(released on July, 2004)
   This sample client written in perl for connection to the blatService
   J2EE_Installation(released on July, 2004)
   Instructions for installing the blatService