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.

Author: Niels Grabe
License: commercial

Use Alibaba2 on this site

BOXSHADE 3.3.1

Boxshade - Pretty Printing and Shading of Multiple-Alignment files

Authors: K. Hofman & M. Baron
Homepage: http://www.ch.embnet.org/software/BOX_form.html
License: freely available

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ClustalW 1.8

ClustalW Multiple Sequence Alignment Program

Authors: J.D. Thompson, D.J. Higgins & T.J. Gibson
Download: ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/License: freely available

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Dialign2.0

Multiple Sequence Alignment Program

Authors: B. Morgenstern, K. Frech, K. Hahn, T. Werner, J. Stoye & A. Dress
License: free only for non-commercial use

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F-Match 1.0

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.
The program reads MATCH output files for the query and control sets. F-Match uses a library of mononucleotide weight matrices
from TRANSFAC^®

Author: Alexander Kel - BIOBASE GmbH

download F-Match

Use F-Match on this site

Match - 1.0 Public

Match^TM is designed for searching potential binding sites for transcription factors (TF binding sites) nucleotide sequences. Match^TM uses a library of mononucleotide weight matrices from TRANSFAC^® 6.0

Authors: Alexander Kel - BIOBASE GmbH, Ellen Goessling - BIOBASE GmbH
License: free for non-commercial use only

Use Match on this site

Search for transcription factors with a certain molecular weight.

Authors: Ingmar Reuter - BIOBASE GmbH, Axel Wagner - BIOBASE GmbH
License: free only for non-commercial use

Use molwSearch on this site

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.

Authors: Dmitry Chekmenev, Carla Haid and Alexander Kel - BIOBASE GmbH

Use P-Match on this site

Search for potential transcription factor binding sites in your own sequences with the pattern search program using TRANSFAC 6.0 public sites.

Authors: Jochen Striepe, Ellen Goessling
License: free only for non-commercial use

Use Patch on this site

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.

Authors: Philip Stegmaier, Alexander Kel, and Edgar Wingender
License: free for use on this site.

Use m2transfac

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.

Authors: Igor Deyneko, Alexander Kel
License: free for use on this site.

Use MatrixCatch on this site

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.
Please, extract all files from the cma.zip file into one directory. Try an example by running cma.bat. To use on your own data, please, run Match first and save the Match output as the ascii flat files.

Authors: Alexander Kel, Tatiana Konovalova, Tagir Valeev, Evgeny Cheremushkin, Olga Kel-Margoulis, Edgar Wingender
Read more about CMA: kel_GCB2005.pdf
License: Web interface to CMA program is free for the use on this site. It is also a part of the commercial system ExPlain™ designed for causal analysis of gene expression data.

Use CMAnalyst on this site

Scanning a Sequence for potential "Polyadenylation Sites".

Authors: K. Hornischer, H. Blöcker
License: free

Use PolyA Scan on this site

ReadSeq reads and writes nucleic/protein sequences in various formats.

Author: D.J. Gilbert
Download: ftp://ftp.bio.indiana.edu/molbio/readseq/version2
License: freely available

Use ReadSeq on this site

Analysis of DNA Sequences for known Eukaryotic Signals

Author: D. Prestridge
Download: ftp://ftp.bio.indiana.edu/molbio/search
License: free

Use SignalScan on this site

Search Tool for Sequence Search in the S/MARt Binder Database

SbBlast makes use of the BLAST Sequence Similarity Search Tool - Version 2.0.13 (May-26-2000).

Author: K. Hornischer, BIOBASE GmbH

Use SbBlast on this site

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.

Author: K. Hornischer, BIOBASE GmbH

Use SnpFind on this site

Use TfBlast on this site