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Match - 1.0 Public

Match is a weight matrix-based program for predicting transcription factor binding sites (TFBS) in DNA sequences. It uses a library of positional weight matrices from TRANSFAC® Public 6.0.

The algorithm is provided here as a standalone online application, working with only a snapshot of TRANSFAC® positional weight matrices from 2005. For a modest academic/non-profit price, subscription to TRANSFAC® Professional provides access to online as well as command line Match tools that work with the complete up-to-date library of TRANSFAC® positional weight matrices. To learn more about TRANSFAC® Professional:

View the unique literature evidence that backs up many TRANSFAC® Professional positional weight matrices
Learn more about the Match command line option
Browse our library of user publications citing TRANSFAC® Professional


Use Match on this site


F-Match 1.0

F-Match is a program for identifying statistically over-represented 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 FASTA DNA sequence entries for the query and control sets. F-Match uses the Match algorithm and a library of positional weight matrices from TRANSFAC®6.0 to scan the input sequences in the two sets for putative TFBSs then compares the experimental and control sets to identify the statistically over-represented TFBSs.

The algorithm is provided here as a standalone application, working with only a snapshot of TRANSFAC® positional weight matrices from 2005. For a modest academic/non-profit price, subscription to the ExPlain™ analysis system provides an end-to-end solution for microarray and ChIP-Seq analysis, integrating the F-Match algorithm with flexible data upload options (Affy, .bed intervals), stored promoter sequences, and the complete up-to-date library of TRANSFAC® positional weight matrices .To learn more about ExPlain™:

Read about analysis of TAL1 ChIP-Seq data in ExPlain™
Browse our library of user publications citing ExPlain™


Use F-Match on this site


Patch 1.0

Patch is a pattern-based program for predicting transcription factor binding sites (TFBS) in DNA sequences. It uses the set of binding sites from TRANSFAC® Public 6.0.

The algorithm is provided here as a standalone online application, working with only a snapshot of TRANSFAC® positional weight matrices from 2005. For a modest academic/non-profit price, subscription to TRANSFAC® Professional download provides access to a command line Patch tool that works with the complete up-to-date library of TRANSFAC® binding sites. Learn more about TRANSFAC® Professional.


Use Patch on this site


P-Match - 1.0 Public

P-Match is a program for predicting transcription factor binding sites (TFBS) in DNA sequences that combines pattern matching and weight matrix approaches. It uses a library of positional weight matrices from TRANSFAC® Public 6.0 along with the site alignments associated with these matrices. Note that unlike Match, P-Match can only use the subset of the matrix libraries for which site alignments are.

The algorithm is provided here as a standalone online application, working with only a snapshot of TRANSFAC® positional weight matrices and site alignments from 2005. For a modest academic/non-profit price, subscription to the ExPlain™ analysis platform provides access to a P-Match tool that works with the complete up-to-date library of TRANSFAC® positional weight matrices and their aligned binding sites. Learn more about the ExPlain™ analysis platform.

Use P-Match on this site


AliBaba 2.1

AliBaba2 is a program, developed by Niels Grabe, for predicting binding sites of transcription factor binding sites in an unknown DNA sequence using binding sites from TRANSFAC® Public.

Use Alibaba2 on this site


Composite Module Analyst (CMA) 1.0

The CMA algorithm reads the output of the 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.

Use CMAnalyst on this site


molwSearch 1.0

Search for TRANSFAC® Public transcription factors by molecular weight.

Use molwSearch on this site


MatrixCatch 2.7

The MatrixCatch algorithm searches for potential composite elements (CEs) for transcription factors (TFs) in any DNA sequence. MatrixCatch uses a library of CE matrix models compiled on the basis of experimentally identified CEs collected in TRANSCOMPEL Public and positional weight matrices for single TF-binding sites collected in TRANSFAC® 6.0 Public.

Use MatrixCatch on this site


SignalScan

The SignalScan algorithm, developed by D. Prestridge, analyzes DNA sequences for known eukaryotic signals.

Download SignalScan

Use SignalScan on this site


SbBlast 1.0

Search the S/MARtDB™ database by sequence.

Use SbBlast on this site


TfBlast 0.1

Search the TRANSFAC® Public Factor Table by protein sequence.

Use TfBlast on this site


VCFmerge 0.1

VCFmerge is a user friendly online interface based on tabix, bgzip, and vcftools. It allows you to upload VCF files of single samples (either in raw or in compressed form) and combine them into a single VCF file that contains all the samples, which you can download.

Use VCFmerge on our COGANGS server




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