Program name  Help  Documentation  Linux  Mac/Windows (W)  Results Viewer  Title 

ReadsMap  View  Download  Download  Download  Reads Mapping Viewer  Mapping of reads to chromosome (contig) 
Reads Mapping Viewer  View  Download  Download  Download   The "Reads Mapping Viewer" software is developed to visualize the "ReadsMap" output data. 
Assembler  View  Download  Download  Download  Assember Viewer  Algorithm of ab initio genome assembling using data produced by nextgeneration sequencing machines (Illumina/Solexa/etc). To view the program output data the Assembler Viewer can be used. 
Assembler Viewer  View  Download  Download  Download   The "Assembler Viewer" software is developed to visualize the "Assembler" output data. 
SNPToolbox  View  Download  Download (4.3Gb)  Download (W) (3.8GB)   A fast and effective tool for analysis of genome variations in human chromosomes. 
Promoter 
CPGFinder  View  Download  Download  Download   Search for CpG islands in sequences 
FPROM  View  Download  Download  Download   Human promoter prediction 
Nsite  View  Download  Download  Download   Search for of consensus patterns with statistical estimation. 
Nsitem  View  Download  Download  Download   Search for regulatory motifs conserved in several sequences 
Pattern  View  Download  Download  Download   Search for significant patterns in the set of sequences. 
Polyah  View  Download  Download  Download   Recognition of 3'end cleavage and polyadenilation region 
ScanWMPL  View  Download  Download  Download   Search for weight matrix patterns of plant regulatory sequences 
TSSG  View  Download  Download  Download   Recognition of human PolII promoter region and start of transcription 
Protein Structure 
3DComp  View  Download  Download  Download  3DExplorer  Sequence Alignment to Superposition 
3DMatch  View  Download  Download  Download  3DExplorer  Pairwise protein structure alignment 
3DModelFit  View  Download  Download  Download  3DExplorer  Program for the estimation of quality of 3D model structure of protein. 
Abini3D  View  Download  Download  Download  3DExplorer  Ab inition folding 
CysRec  View  Download  Download  Download   Prediction of SSbonding states of cysteines and disulphide bridges in protein sequences 
GetAtoms  View  Download  Download  Download  3DExplorer  Optimization of replaced side chain groups by simulated annealing algorithm 
MolDyn  View  Download  Download  Download  3DExplorer  MolDyn is designed to perform multiple tasks with protein structure. 
MolMech  View  Download  Download  Download  3DExplorer  Energy minimization program by molecular mechanic 
NNSSP  View  Download  Download  Download   Nearestneighbor SS prediction 
NetSSPredict  View  Download  Download  Download   Program for secondary structure prediction. Neural nets based on profile of psiBLAST comparison of the query sequence with NR database. 
PDisorder  View  Download  Download  Download   Program for predicting ordered and disordered regions in protein sequences 
SSEnvID  View  Download  Download  Download   Protein secondary structure and environment assignment from atomic coordinates 
SSP  View  Download  Download  Download   Prediction of ahelix and bstrand segments of globular proteins 
SSPAL  View  Download  Download  Download   Prediction of protein secondary sturcture by using local alignments 
Alignments 
Protmap  View  Download  Download  Download   Mapping of a set of proteins on genome 
MaliN  View  Download  Download  Download  MaliN Viewer  Multiple alignment for nucleotide sequences. 
MaliP  View  Download  Download  Download  MaliP Viewer  Multiple alignment for protein sequences. 
EstMap  View  Download  Download  Download   Program for mapping a whole set of mRNAs/ESTs to a chromosome sequence 
Scan2  View  Download  Download  Download   Program for aligning two multimegabytesize genome sequences using a sequential search for most significant similarity regions. 
Scan2a  View  Download  Download  Download   Program for aligning two aminoacid sequences using a sequential search for most significant similarity regions. 
Gene Finding 
Fex  View  Download  Download  Download   Prediction of internal, 5' and 3' exons in Human DNA sequences. 
Fgenes  View  Download  Download  Download  Sequence Explorer,PDFGenes  Pattern based human gene structure prediction (multiple genes, both chains). 
Fgenesm  View  Download  Download  Download  Sequence Explorer,PDFGenes  Patternbased prediction of multiple variants of gene structure 
Fsplice  View  Download  Download  Download   Program provides the possibility to search for both donor and acceptor sites, and to define thresholds for them independently. Program allows to search minor variants of splicing donor site (GCsite) as well. 
PDFGenes  View  Download  Download  Download   PDFGenes utilizes the results of Gene Finding software, such as FGenesh, FGenesh+,FGeneshC, FGenesh2, FGenes, FGenesmand BestORF, and represents them in PDF format for better viewability. 
PSF  View  Download  Download  Download   Finding pseudogenes in a genomic sequence. 
Rnaspl  View  Download  Download  Download   Program for predicting exonexon junction positions in cDNA sequences. For this program gcc fortran library should be installed locally. 
SPL  View  Download  Download  Download   Prediction of splice sites in DNA sequences. For this program gcc fortran library should be installed locally. 
SplM  View  Download  Download  Download   Prediction of splice sites in Human DNA sequences. 
Bacterial Gene Finding 
ABSplit  View  Download  Download  Download  Sequence Explorer  Program determines for the nucleotide sequence of approx. 300600 n.p. whether it belongs to archeal or bacterial genome. 
Bprom  View  Download  Download  Download   Prediction of bacterial promoters 
FindTerm  View  Download  Download  Download  RNA Secondary Structure Viewer  Searchs for bacterial terminators in DNA sequences. 
RNA Strucuture 
BestpalE  View  Download  Download  Download   Calculates best palindrome for given RNA sequence, and also a set suboptimal palindromes (sorted by energy) 
BestpalH  View  Download  Download  Download  RNA Secondary Structure Viewer  Calculates best palindrome for given RNA sequence with restrictions. 
BestpalW  View  Download  Download  Download  RNA Secondary Structure Viewer  Program for searching best "linear" RNA secondary structure for long sequences with a window moving along the sequence. 
FindmiRNA  View  Download  Download  Download   Searchs for premiRNAs in a given RNA sequence and for miRNA in each found premiRNA. 
FoldRNA  View  Download  Download  Download  RNA Secondary Structure Viewer  Program for RNA secondary structure prediction based on dynamic programming (Nussinov and Jackonson, 1978, Zuker, 2005). 
Protein Location 
PSite  View  Download  Download  Download   Search for of prosite patterns with statistical estimation. 
CTLEpitope  View  Download  Download  Download   This program is designed for prediction of CTL epitopes of length=9 in protein sequences. 
ProtcompAN  View  Download  Download  Download   Program for Identification of subcellular localization of Eukaryotic proteins: Animal/Fungi. 
ProtcompB  View  Download  Download  Download   Program for Identification of subcellular localization of bacterial proteins. 
ProtcompPL  View  Download  Download  Download   Program for Identification of subcellular localization of Eukaryotic proteins: Plants 
Repeats 
LCRep  View  Download  Download  Download  Sequence Explorer  Program for mapping low complexity regions in nucleotide sequences. 
LCRepP  View  Download  Download  Download  Sequence Explorer  Program for mapping low complexity regions in protein sequences. 
TandemRep  View  Download  Download  Download   Program for mapping the Tandem Repeats Regions in nucleotide sequences. 
TandemRepP  View  Download  Download  Download   Program for mapping the Tandem Repeats Regions in protein sequences. 
SelTag 
BdClust  View  Download  Download  Download   Clustering of gene expression profiles or samples by BenDor algorithm. 
CHPImport  View  Download  Download  Download   Import expression data from the Affymetrix CHP format to SelTag data file. 
FieldCorr  View  Download  Download  Download  Graph Viewer  The program calculates correlation coefficients between the gene expression values in experiments (fields). 
GeneCorr  View  Download  Download  Download  Graph Viewer  The program calculates correlation coefficients between the gene expression profiles. 
HClust  View  Download  Download  Download   Clustering of gene expression profiles by hierarchical algorithm. 
Mas5Norm  View  Download  Download  Download   Normalization of the Affymetrix gene expression row data by MAS 5.0 algorithm. 
Mas5Baseline  View  Download  Download  Download   Comparison of the Affymetrix gene expression row data to the baseline data by MAS 5.0 algorithm. 
SelByExpr  View  Download  Download  Download   Gene selection by query (logical expression). 
SelCorr  View  Download  Download  Download  Graph Viewer  The program selects most correlated genes for specified gene set. 
SOMClust  View  Download  Download  Download   The program clusters gene expression profiles or samples by SOM (SelfOrganizing Map) algorithm. 
Statistics 
SNNBPLearn  View  Download  Download  Download   SNNBPLearn implement the backpropagation training algorithm and output the optimal NN structure, saved in the SNNBP internal format. 
SNNBPPredict  View  Download  Download  Download   SNNBPPredict  neural network calculate output values (predictions) using input values from the data file (target values need not be specified in this option). 
SNNBPTest  View  Download  Download  Download   SNNBPTest implement testing of the previously obtained network on the user data. 
Seqman 
Restrictase  View  Download  Download  Download  Restrictase Viewer  The program for finding and displaying the positions of the cut sites of restriction enzyme recognition sequences. 
Viewers 
3DExplorer  View  Download  Download  Download   3D Explorer is designed to visualize spatial models of biological macromolecules and their complexes. Application is compatible with PDB files. 
Assembler Viewer  View  Download  Download  Download   The "Assembler Viewer" software is developed to visualize the "Assembler" output data. 
DotPlot viewer  View  Download  Download  Download   DotPlot viewer provides the possibility to visualize the sites of homology between the sets of sequences. 
Graph  View  Download  Download  Download   The application is made for visualization of statistics files. 
MaliN Viewer  View   Download  Download   The "MaliN viewer" application is developed for aligning nucleotide sequences and working with results of such alignments. 
MaliP Viewer  View   Download  Download   The "MaliP viewer" application is developed for aligning protein sequences and working with results of such alignments. 
Reads Mapping Viewer  View  Download  Download  Download   The "Reads Mapping Viewer" software is developed to visualize the "ReadsMap" output data. 
Restrictase Viewer  View  Download  Download  Download   The "Restrictase viewer" application is purposed for visualization of restriction sites that were found with use of "Restrictase" program. 
RNA Secondary Structure Viewer  View  Download  Download  Download   RNA Secondary Structure Viewer is made for visualization and manipulation of RNA secondary structure. 
Sequence Explorer  View  Download  Download  Download   Sequence Explorer provides the visual representation of genome annotations. 