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.
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.
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.
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.
Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparisonYou can access it online directly at BMC Bioinformatics.
Brown CT, Xie Y, Davidson EH, and Cameron RA.
BMC Bioinformatics 2005, 6:70. 24 Mar 2005. (PubMed ID: not yet assigned)
The original publication describing FamilyRelations and SeqComp is:
New computational approaches for analysis of cis-regulatory networks.The first biological analysis done based on FamilyRelations and SeqComp results is detailed in:
Brown et al.
Dev Biol. 2002 Jun 1;246(1):86-102. (PubMed ID: 12027436)
Patchy interspecific sequence similarities efficiently identify positive cis-regulatory elements in the sea urchin.Martha Kirouac and Paul Sternberg used FamilyRelations and SeqComp to help dissect regulatory regions in C. elegans:
Yuh et al.
Dev Biol. 2002 Jun 1;246(1):148-61. (PubMed ID: 12027440)
cis-Regulatory control of three cell fate-specific genes in vulval organogenesis of Caenorhabditis elegans and C. briggsae.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:
Kiruoac & Sternberg
Dev Biol. 2003 May 1;257(1):85-103. (PubMed ID: 12710959)
Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation.Thomas Leung used FamilyRelationsII and paircomp to check conservation of NFKB binding sites between human/mouse:
Romano & Wray
Development. 2003 Sep;130(17):4187-99. (PubMed ID: 12874137)
One nucleotide in a kappaB site can determine cofactor specificity for NF-kappaB dimers.One additional paper from the Cho Lab (frog-mouse comparison) has not yet been published.
Leung et al.
Cell. 2004 Aug 20;118(4):453-64. (PubMed ID:: 15315758)
Titus Brown has also written a short (unpublished) article on the math of fixed-width window pairwise matches; you can download it here.
SeqComp is written in C++ and should compile with any modern C++ compiler.
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.
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.