Main Products

Most of our programs are available for different Unix platforms with or without source codes, unless noted otherwise, with data files for dozen different organisms. Data files for new organisms or taxonomic groups can be constructed by a special order. Complete list of products is available upon request.

Gene Prediction, Best ORF and Splice sites, NON-Standard splice sites Identicication

Functional Sites, Promoter Prediction

DBSCAN, Scan2, RNA_MAP, OLIGO_MAP, ESTS_MAP - Database Search, Genome Comparison and RNA/EST/OLIGO mapping Programs

GeneParse - Sequence Database Parsing Software

GeneExplorer - Tool for Analysis of Expression Data

Psite - Program for Identification of Significant Prosite Patterns

ProtComp - Program for Identification of sub-cellular localization of Eukaryotic protein (10 compartments)

Gene Prediction Programs

FGENES
Algorithm based on pattern recognition of different types of exons, promoters and polyA signals. Optimal combination of these features is then found by dynamic programming and a set of gene models is constructed along given sequence. One of the most popular gene finders available.

FGENES-M
FGENES variant that outputs several alternative gene structures. Useful for predicting alternative splicing or providing several gene variants for subsequent experimental testing.

FGENESH
Hidden Markov Model (HMM)-based gene prediction program. Along with FGENES, one of the most popular gene predictors available.

FGENESH+
FGENESH variant that uses information on homologous existing proteins for more accurate gene assembly from predicted exons.

FGENESH_C
Add-on to FGENESH that uses information on homologous cDNA/EST for more accurate gene assembly from predicted exons.

FGENESH-2
Variant of FGENESH that uses two homologous genomic DNA sequences, such as Human and mouse, for more accurate gene prediction.

SPL and SPLM
Programs for splice site identification, SPLM includes finding NON-standard splice sites such as GC-donor site or AT-AC sites.

Functional Site Prediction Programs

TSSW/TSSG
Two programs for predicting PolII promoter regions. Use linear discriminant function combining characteristics describing functional motifs and oligonucleotide composition of transcription start sites. TSSW uses Wingender's functional site database, while TSSG uses data of Dan Prestridge.

POLYAH
PolyA site prediction program. Uses linear discriminant functions combining characteristics describing various contextual features of polyA sites.

NSITE
Program for analysis of regulatory regions and composition of their functional motifs.Based on statistical estimation of expected number of a nucleotide consensus pattern in a given sequence. Uses datafile consisting of public release of Transfac sequences and a set additional functional motifs.

DBSCAN and SCAN2- Database Search and Genome Comparison Programs

DBSCAN performs search of DNA sequence through database in a a BLAST-like manner, except that it can handle multimegabyte-sized sequences.

SCAN2 performs alignment of two multimegabyte sequences.

Both programs have Java viewer for easy visualization and parsing of results.

New program RNA_MAP is one of group (including ESTS_MAP, OLIGO_MAP and DBSAN). This group is devoted to comparisons with long genomic sequences 20-300 MB.
RNA_MAP is a fast algorithm to accurately map mRNA sequence to genomic sequence taking into account splice sites flanking intron sequences. Time to map mRNA 300 bp on 52 of unmasked MB Y chromosome is about 19 sec, for 7300 bp the time about 47 sec (checked both chains, one DEC alpha processor 500 Mz).

EST_SMAP is for mapping the whole set to a chromosome sequence. For example, 11000 sequences of full mRNA from NCBI reference set are mapped to 52 MB of unmasked Y chromosome for about 18-25 min (depending on computer memory size).

OLIGO_MAP is designed to map a set of oligonucleotides used for microarray production. The program map 300000 oligos 25-30 bp long on 49 MB of unmasked Chromosome 22 for 8 min. Program is useful to check location of oligos and their uniqueness in genome.

GeneParse - Sequence Database Parsing Software
GeneParse takes information from GeneBank or EMBL databases and creates a new, gene-centered database, InfoGene, where information from different GenBank entries about a particular gene is combined in one record of InfoGene database

GeneExplorer - Tool for Analysis of Expression Data

Psite - Program for Identification of Significant Prosite Patterns

ProtComp - Program for Identification of sub-cellular localization of Eukaryotic protein
The program is based on complex neural-network recognizers, which identify probability of he subcellular localization in Nuclear, Plasma membrane, Extracellular, Cytoplasmic, Mitochondrial, Chloroplast, Endoplasmic reticulum, Peroxisomal, Lysosomal or Golgi compartments.