FamilyJewels

Tools for Comparative Sequence Analysis

This is the home page for the FamilyJewels project at Caltech, where we are developing tools for biologists to do comparisons of genomic DNA on the order of 10-100kb in length.

New users should start with the introduction to doing comparative sequence analysis with FamilyRelations II.

If you are interested in motif searching, the Cartwheel server now lets users build position-weight matrices and search their own sequences with them. We have a short video demonstration (MP4 format) of this functionality.

There are two example class projects available for people interested in using FRII for a genomics class. They were both developed for classes at Caltech.

Announcements:

Methods paper. A paper discussing techniques for cis-regulatory bioinformatics is now available: Computational Approaches to Finding and Analyzing cis-Regulatory Elements.

Software update. There is a new version of FamilyRelationsII that fixes one or two crashing bugs. Go check it out! -- August 26th, 2005

A paper on FamilyRelationsII and paircomp has been published: Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison. Get the article at BMC Bioinformatics (Open Access). -- Mar 24, 2005

paircomp 1.0 released! This release makes the analysis functionality of paircomp completely available to C++ and Python programmers. Read the docs and/or download paircomp. -- Mar 22, 2005

As of November 2004, Cartwheel/FRII can execute and display Vista- and PipMaker-style comparisons, in addition to the regular dot-plot-style comparisons.

Software

FamilyRelations II, a.k.a FRII, is a graphical viewer for analyses created using the Cartwheel analysis server. FRII is available for Windows, Mac OS X, and Linux; you can download it here.

The paircomp toolkit is a replacement for SeqComp; it provides a C++ and Python interface to do fixed-width window analyses of two DNA sequences. You can read the documentation for paircomp and download the toolkit here.

Both FRII and paircomp are actively maintained by Titus Brown, as part of his tools for sequence analysis.

Related Projects:

SeqComp is the program originally used to run the comparisons displayed by FamilyRelations; it was written by Tristan De Buysscher. Its functionality has since been integrated into Mussa, Tristan's n-way sequence comparison system. SeqComp is still available but is not supported.

FamilyRelations is the Java/Jython predecessor to FamilyRelationsII. It is no longer functional, but the source code is still available through SourceForge.

Dr. Shoudan Liang, a physicist from NASA, wrote find_patch, a version of SeqComp that is highly optimized for small windowsizes. It is available but not supported; eventually, the optimizations will be incorporated into the paircomp toolkit.


Additional Information

Software Availability

All of this software is freely and openly available under either the GPL or LGPL. Please see the individual distributions for details.

Publications

The canonical publication describing FamilyRelationsII, paircomp, and Cartwheel is:
Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison
Brown CT, Xie Y, Davidson EH, and Cameron RA.
BMC Bioinformatics 2005, 6:70. 24 Mar 2005. (PubMed ID: not yet assigned)
You can access it online directly at BMC Bioinformatics.

The original publication describing FamilyRelations and SeqComp is:

New computational approaches for analysis of cis-regulatory networks.
Brown et al.
Dev Biol. 2002 Jun 1;246(1):86-102. (PubMed ID: 12027436)
The first biological analysis done based on FamilyRelations and SeqComp results is detailed in:
Patchy interspecific sequence similarities efficiently identify positive cis-regulatory elements in the sea urchin.
Yuh et al.
Dev Biol. 2002 Jun 1;246(1):148-61. (PubMed ID: 12027440)
Martha Kirouac and Paul Sternberg used FamilyRelations and SeqComp to help dissect regulatory regions in C. elegans:
cis-Regulatory control of three cell fate-specific genes in vulval organogenesis of Caenorhabditis elegans and C. briggsae.
Kiruoac & Sternberg
Dev Biol. 2003 May 1;257(1):85-103. (PubMed ID: 12710959)
Laura Romano and Greg Wray used FamilyRelations and SeqComp to display a comparison of the Endo16 cis-regulatory region done between two species of sea urchin:
Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation.
Romano & Wray
Development. 2003 Sep;130(17):4187-99. (PubMed ID: 12874137)
Thomas Leung used FamilyRelationsII and paircomp to check conservation of NFKB binding sites between human/mouse:
One nucleotide in a kappaB site can determine cofactor specificity for NF-kappaB dimers.
Leung et al.
Cell. 2004 Aug 20;118(4):453-64. (PubMed ID:: 15315758)
One additional paper from the Cho Lab (frog-mouse comparison) has not yet been published.

Titus Brown has also written a short (unpublished) article on the math of fixed-width window pairwise matches; you can download it here.

Old Software

The original version of FamilyRelations, "FR I", was written in Java/Jython by Titus Brown. It runs under Java Web Start. While it is still available, it's not supported any more; see FRII, above.

Information for Developers

The source code for all of the software on this page is available under either the GPL or the LGPL. This means that anyone can use, modify, and redistribute the source code and software, as long as they make the source code (with modifications) available to others.

SeqComp is written in C++ and should compile with any modern C++ compiler.

FamilyRelations is written in Jython, a Python interpreter written in Java. It uses Java Swing extensively.

find_patch is written in C++.

FRII is written in C++ and uses the FLTK graphics toolkit.

The paircomp toolkit is written in C++ and contains an embedding for Python.

Software Credits

Tristan De Buysscher wrote the SeqComp program under the guidance of Barbara Wold. Shoudan Liang wrote the find_patch program in collaboration with Titus Brown and Eric Davidson. Titus Brown developed FamilyRelations, FRII, and paircomp under the supervision of Eric Davidson; Ramon Cendejas and Madeleine Price also worked on the original FamilyRelations.

Andy Cameron and Erich Schwarz were two early adopters of FamilyRelations who contributed extensively to its design.

Eric Davidson and Barbara Wold advised Titus and Tristan, respectively.

The Cartwheel contributors page has more detailed information on who did what.

Last updated March 2005