DFCI Gene Indices Software Tools |
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The Gene Indices group is committed to making software tools freely available to the scientific community. The software provided on this page represents modified versions of our internal software, designed to run independently of the operating system environment (e.g. not linked to the database and software environment at DFCI). This software is available free of charge under the Artistic License; download and use of this software constitutes agreement to abide by the terms of the Artistic License. If you would like to be notified about software updates, please click on the package logo and fill in your contact information. The Gene Index Project and tools is supported in part by funding from the US Department of Energy, Grant #DE-FG02-99ER62852, and the US National Science Foundation, Grant #DBI-9983070. Additional funds are provided by the US National Science Foundation through grants #DBI-9813392 and #DBI-9975866.
This package automates clustering and assembly of a large EST/mRNA dataset. The clustering is performed by a slightly modified version of NCBI's megablast , and the resulting clusters are then assembled using CAP3 assembly program. TGICL starts with a large multi-FASTA file (and an optional peer quality values file) and outputs the assembly files as produced by CAP3. Both clustering and assembly phases can be parallelized by distributing the searches and the assembly jobs across multiple CPUs, as TGICL can take advantage of either SMP machines or PVM (Parallel Virtual Machine) clusters. The two full precompiled packages below were built on Linux and SunOS, respectively. They include CAP3, mgblast and all the other binaries for this platform (of course, except the base Unix utilities like 'sed', 'sort' etc.). Please note that only the Linux version was thoroughly tested at DFCI.
The platform independent perl scripts can also be downloaded separately
from tgicl_scripts.tar.gz.
These scripts are likely to be updated more often, as opposed to
the binaries which are rather stable. In such cases there is no need to
download again the full, large packages provided above, although
they also include these scripts.
Please note that the entire project is hosted at sourceforge.net where you can find all previous versions including the source code. Just click on View all Files button and browse all versions listed there. GICL For advanced users, a more complex version of TGICL that has its own custom incremental assembler and extensive grid support (SGE and Condor), can be downloaded here:
If you want to build these programs from source, the C++ source code
for most of the tools is provided below. We do not include here the source code
for CAP3 and for the formatdb utility and other standard BLAST-related tools that are part of the
NCBI Toolkit
Please note that in order to compile mgblast, a specific
version of the NCBI Toolkit is needed (the C version, not the C++ one; check the README file in the 'mgblast' source package
below for the specific version of the NCBI Toolkit that should be installed). CAP3 is closed source but one can and
should download the latest public binary build for the target platform in order to use it with TGICL.
The author of CAP3, Dr. Xiaoqiu Huang,
may be contacted for CAP3-specific issues, and currently the CAP3 binary for multiple platforms can be downloaded from:
http://seq.cs.iastate.edu/cap3.html
The following utilities depend on a set of C++ utility classes and functions, a genomic C++ library (gclib) which should be downloaded first in order to compile them.
This is a graphical, interactive tool for inspecting the ACE format assembly files generated by
CAP3 or phrap. Beasides the ACE files, the program also supports a custom cluster layout format
for the overview of a possible multiple alignments generated just from pairwise alignments,
where no detailed nucleotide level alignment is needed and provided. The
"containment clustering" program (nrcl) mentioned in the TGI Clustering
tools(TGICL) above can generate such a "cluster layout" file (*.lyt).
Here is a precompiled linux version with the required dynamic FOX library included:
clview_linux_i386.tar.gz
The program was built using the FOX toolkit by Jeroen van der Zijp,
a portable and feature-rich C++ framework for developing graphical user interfaces under Unix and Windows.
In order to compile the source code of this viewer,
you need to download and install the FOX library
Precompiled Linux versions can be found here: seqclean.tar.gz (32-bit). There is also a 64 bit version seqclean_x86_64.tar.gz. Please see the README file first. Please note there is no contaminant database included in the package - you need to provide your own screening files or download and format a generic vector database like NCBI's UniVec. The package also doesn't include NCBI's blastall and megablast utilities which you should obtain from the NCBI site (their full source is included in the NCBI C Toolkit). The C/C++ source for the other programs in the package can be found in gclib package:
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DAS/XML Genomic Viewer
The Genomic viewer borrows modules from http://www.biodas.org (lstein@cshl.org) & http://webreference.com.
The application is in constant flux and development and may not up fully compliant with the current DAS protocol all the time. For specific feature requests or programming questions please write directly to the author (Geo Pertea). For DAS Comments/Questions send mail to (Foo Cheung). |
| Acknowledgements | |
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The Gene Index Project is supported in part by funding from the US National Science Foundation through grant #DBI-0552416. |
 
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