Computer Programs

GArna: Predicting 2D structure of RNA by genetic algorithm

ReClus - description of new program for prediction of regulatory region clusters in large DNA sequences

Protein domain recogintion by properties

search the direct, inverse, complementary and symmetric substring copies (repeats) in a target DNA sequence;
visulaize the results obtained in 1) with the help of Java-designed viewer applet. The repeats searched are subject to the statistical significance based on the binomial distibution ). The repeats with the length exceeding the significance threshold (0.05) are considered only

RGSiteScan program: This program is designed to predict the potential binding sites of 37 transcription factors in the target DNA sequence.

RecGroup program:This program is aimed on construction of Recognition groups which are used further by the <RGSiteScan> for final result, that is a revealing of potential binding sites in a DNA sequence. So, this is the first program in a two-stage process of transcription factor binding sites revealing.

POLIIISCAN - POL III PROMOTER RECOGNITION: brief description of the computer program POLIIISCAN.

Predicting activities of functional sites in DNA/RNA

(CRASP) - Correlation Analysis of Sequences of Proteins

CRAFT) - DNA Bending Stiffness Features

Educational programs

Life is just a game...

Unsorted programs

VMM : Variable memory Markov model for nucleosome formation site prediction

SiteGA Site Recognition by Genetic Algorithm

SiteCon

ProGA - Eukaryotic Promoters Recognition by Genetic Algorithm

Phase - index for phased dinucleotide probabilities

Recognition of transcription factor binding sites by trinucleotide weight matrix

Complexity decomposition of genetic texts by modified Lempel-Ziv method

LowComplexity: Sequence analysis software

Leader mRNA - Predicting expression level of an eukaryotic gene for following taxons

ddG-Matrix: Regulatory Protein binds DNA with single nucleotide substitutions

Promoter classification

BinomSite – transcription factor binding sites recognition program

Analysis of mRNA secondary structure at the translation start site region: Prediction of compensatory downstream hairpin increasing translation from AUG codon in suboptimal context

Blast search ASPD database

Transgene - Programs for prediction of mRNA translational activity

GibbsSampler - program for local multiple alignment for nucleotide sequences

bDNA - bDNA Profiles

Cons - Precise Recognition by Consensus

Freq - Precise Recognition by frequency matrix

GC_Net - Complexity Profile Builder

Nc_Pro - Nucleotide Profile Builder

Prof_Pat is a collection of patterns constructed for protein families

EAGLE (Expanded Alignment at Genome LEvel) - under construction

kpoxa - demo version of MOLKERN package