Programs |
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| AliBaba
2.1 AliBaba2 is a program for
predicting binding sites of transcription factor binding sites
in an unknown DNA sequence. Therefore it uses the binding sites
collected in TRANSFAC. AliBaba2 is currently the most specific
tool for predicting sites. |
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| BOXSHADE
3.3.1 Boxshade -
Pretty Printing and Shading of Multiple-Alignment files |
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| ClustalW
1.8 ClustalW Multiple
Sequence Alignment Program |
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Multiple Sequence Alignment Program |
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F-MATCH is a program for identifying statistically
overrepresented Transcription Factor Binding Sites (TFBS) in a
set of sequences compared against a control set, assuming a binomial
distribution of TFBS frequency. |
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MatchTM is designed for searching potential
binding sites for transcription factors (TF binding sites) nucleotide
sequences. MatchTM uses a library of mononucleotide
weight matrices from TRANSFAC® 6.0 |
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Search for transcription factors with a certain
molecular weight. |
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P-Match is a new tool for identifying transcription
factor binding sites (TF binding sites) in DNA sequences. It combines
pattern matching and weight matrix approaches thus providing higher
accuracy of recognition than each of the methods alone. P-Match
uses a library of mononucleotide weight matrices from TRANSFAC®
6.0 along with the site alignments associated with these matrices.
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Search for potential transcription factor binding
sites in your own sequences with the pattern search program using
TRANSFAC 6.0 public sites. |
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m2transfac is a PWM-PWM alignment interface for
the TRANSFAC(R) database. For given user motifs, m2transfac reports
all non-overlapping pairwise alignments to a TRANSFAC(R) matrix
which satisfy a specified threshold. |
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The MatrixCatch tool is designed for searching
potential composite elements (CEs) for transcription factors (TFs)
in any DNA sequence, which may be of interest. MatrixCatch uses
a library of CE matrix models, which were compiled on a basis
of experimentally identified CEs collected in TRANSCOMPEL©
database and mononucleotide weight matrices for single TF-binding
sites collected in TRANSFAC 6.0 public database. |
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Composite Module Analyst (CMA) 1.0 CMA reads output of Match program
and applies a genetic algorithm in order to define promoter models
based on the composition of transcription factor binding sites
and their pairs. |
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Scanning a Sequence for potential
"Polyadenylation Sites". |
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ReadSeq reads and writes nucleic/protein
sequences in various formats. |
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Analysis of DNA Sequences for known
Eukaryotic Signals |
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Search Tool for Sequence Search in
the S/MARt Binder Database |
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SNPFIND is a tool for searches in
the Database of Single Nucleotide Polymorphisms. The search algorithm
used for the database search is the BLAST algorithm. |
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Search Tool for Sequence Search in
the TRANSFAC Factor Table |
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