Table 1 Gene Regulation Prediction Software utilised

CPGPLOT

CpG island detection

http://www.ebi.ac.uk/emboss/cpgplot

TESS, Transcription Element Search System

PSSM-based TF binding site search

http://www.cbil.upenn.edu/tess

Matinspector

PSSM-based TF binding site search

http://www.genomatix.de/products/MatInspector/index.html

MATCH and P-MATCH

PSSM-based TF binding site search

http://www.gene-regulation.com/pub/programs.html#match

TSSG

TSS Prediction

http://www.softberry.com

NNPP, Neural Network Promoter Prediction

Uses Neural Networks to predict basal promoter region and TSS.

http://www.fruitfly.org/seq_tools/promoter.html

Promoter Scan

TSS prediction, limited to TATA class promoters

http://thr.cit.nih.gov/molbio/proscan/analysis.html

Promoter 2.0

Uses Neural Networks with Genetic Algorithms to predict vertebrate PolII promoters regions.

http://www.cbs.dtu.dk/services/Promoter

PromoterInspector

Context-based prediction of eukaryotic pol II promoter regions.

http://www.genomatix.de/cgi-bin/promoterinspector_pd/promoterinspector.pl

McPromoter

Markov Chain/Neural net based Promoter and TSS prediction program

http://genes.mit.edu/McPromoter.html

MAPPER

HMM based cis-element search, lists interacting TFs (promoter modules) and TF class summary

http://mapper.chip.org

NCBI Entrez Gene

Searchable database of genes

http://www.ncbi.nih.gov/entrez

Cister, Cis-element Cluster Finder

HMM based cis-element cluster search

http://zlab.bu.edu/~mfrith/cister.shtml

RVista 2.0

Phylogenetic footprinting, combines database searches with comparative sequence analysis.

http://rvista.dcode.org

MAR-Wiz

S/MAR motif sequence search

http://futuresoft.org/modules/MarFinder/index.html