Bagel is an a new AJAX web browser that lets you view a database of existing annotation tracks as well as upload your own.
Tandem Repeats Finder is an application for finding tandem repeats in DNA sequences. It employs a stochastic model of repeats and
associated statistical detection criteria. It is extremely fast and thorough,
and is now regularly used to analyze new genomic sequences (see the UCSC Golden Path human genome browser for example).
Tandem repeats are ubiquitous sequence features in both prokaryotic and
eukaryotic genomes. In humans, they are known to cause at least ten inherited
neurological diseases including fragile-X mental retardation, Huntington's
disease, and myotonic dystrophy and are associated with a number of other major
illnesses, including diabetes, epilepsy, and ovarian and other cancers.
Additionally, they are the basis of DNA fingerprinting and have recently been
used to discriminate between different bacterial strains, including
Composition Alignment or, more whimsically, scrambled alignment, employs the mechanisms of string matching and string comparison yet avoids the overdependence of those methods on position-by-position matching. In composition alignment, we extend the matching concept to composition matching. Two strings have a composition match if their lengths are equal and they have the same nucleotide content.
Tandem Repeats Database (TRDB) is a public repository of information about tandem repeats in multiple genomes. Additionally, it provides private workspace for researchers to use the
Tandem Repeats Finder with added features. For example, it can store all of the repeats found in a sequence (as well as the original sequence) in a convenient manner for later processing.
The repeats are organized into sets. A variety of tools are available for additional processing:
1) clustering repeats into families,
2) predicting copy number polymorphism based on sequence characteristics,
3) annotation of repeats and families,
4) advanced filtering capabilitites,
5) data visualization, and
6) data downloading.
Repeats Finder is an application very similar
to the Tandem Repeats Finder. It searches for Inverted Repeats. We have set up a
Repeats Database (IRDB) web interface where you can try it out (you must register, can't run it though a guest account.) It can store
repeats and sequences and has many of the filtering
capabilities of TRDB. There is also a convenient
graphical interface for viewing alignments.
Fold Support is a tool that can be used to evaluate
a predicted RNA structure based on the mutations
present in a given number of alleles.
is a tool to identify conserved codons where the
amino acid permits 4-fold degeneracy on the third
is a program that accepts repeat(s) in the TRF .dat
file format and reconstructs duplication histories
as described in [G. Benson and L. Dong, Reconstructing
the Duplication History of a Tandem Repeat,
Proceedings of the Seventh International Conference
on Intelligent Systems for Molecular Biology (ISMB-99)].
The output is a value, HistoryR, which can be used
to predict length polymorphism as reported in [F.
Denoeud, G. Vergnaud and G. Benson, Predicting
Human Minisatellite Polymorphism, 2002 (submitted
for publication)]. This feature is also available
Mutation Master accepts a multiple alignment data file (.MSF) and rapidly provides a
visual display and tabulation of site, frequency, number and likelihood of point
mutations. Alignment of many related sequences from viral or bacterial quasi-species can
reveal important information about proteins, RNA, and DNA, including changes
that correlate with pathogenicity, drug susceptibility and sequence structure.
Extracting this information, manually, from multiple alignments is often
difficult, especially when a large number of long sequences are utilized.
Analysis of hepatitus C virus (HCV) protein sequences using Mutation
Master has identified possible sites of amino acid structural interaction, and
has revealed that ARFP, a novel protein encoded in an overlapping reading frame,
is as conserved as conventional HCV proteins. See the paper J. Walewski, J. Gutierrez, W. Branch-Elliman, D. Stump, T. Keller, A. Rodriguez, G. Benson, and A. Branch. Mutation Master: Profiles of Substitutions in Hepatitis C Virus RNA of the Core, Alternate Reading Frame and NS2 Coding Regions, RNA 8:557-571, 2002.
Ongoing work includes developing similar tools to analyze RNA multiple alignments for structural clues including
Sequence Alignment Tool is a web
interface to our sequence alignment library. You can submit 2 sequences and align them using various parameters and alignment algorithms. Composition Sequence Alignment Tool is a more composition oriented alignment tool.
Sequence Fraction Tool is useful to cut out a fraction of a sequence at a specified base position.
1st Order Markov Chain Tool is a
tool to generate a probobility file based on a submitted DNA sequence. That file can then be used generate a compatible Random Sequence using the next tool.
Random Sequence Generator will
give you a random sequence(s) of any size.
RNKP is a tool to calculate the probability of run of K heads in the string of length N with a probability of a head set to P.
Synthetic Sequence Creator Tool is useful to create a list of FASTA sequences with planted homologous pairs.
K'nex DNA Models is an educational website on how to build your own DNA models. Targeted for students in middle school, high school and college.