Gene Finding in Eukaryota
FGENESH - HMM based Gene structure prediction
FGENES - Pattern based Human Gene structure
FGENES-M - Multiple variants of Gene structure
FGENESH-M - Prediction of multiple (alternative splicing) variants of potential genes in genomic DNA
FGENESH_GC - (with possible donor GC) HMM based Human Gene structure prediction
BESTORF - Finding coding fragment EST/mRNA
FEX - Finding potential 5'-, internal and 3'-coding exons
SPL - Search for potential splice sites
SPLM - Search for non-standard splice sites using weight matrices
RNASPL - Search for exon-exon junction positions in cDNA
FSPLICE - Find splice sites in genomic DNA
Gene finding with similarity
FGENESH+ - HMM plus similar protein-based gene prediction
Speed and Accuracy of Fgenesh+
PROT_MAP - mapping of a set of proteins on genome
FGENESH_C - HMM plus similar cDNA-based gene structure prediction
FGENESH-2 - HMM gene prediction with two sequences of close organisms
Operon and Gene Finding in Bacteria
FGENESB - Operon and Gene finding in Bacteria
BPROM - Promoter finding in Bacteria
AbSplit - Separating archea and bactrial genome fragments
FindTerm - Finding Terminators in bacterial genomes
Annotations /all bacteria
Gene Finding in Viral Genomes
FGENESV - Gene finding in Viral Genomes (Trained Pattern/Markov chain-based viral gene prediction)
FGENESV0 - Gene finding in Viral Genomes (Generic parameters Markov chain-based viral gene prediction)
GenomeSequence Explorer Infogene
Human GenomeSequence Explorer - Visualization of Human genome information -> (Apr. 10, 2003 (hg15) )
Mouse GenomeSequence Explorer - Visualization of Mouse genome information (Feb. 2003 (mm3) )
Rat GenomeSequence Explorer - Visualization of Rat genome information (Jun. 2003 (rn3) )
Bacterial GenomeSequence Explorer - Visualization of Bacterial genomes information
Infogene database of Known genes of many organisms (August2001)
SpliceDB - Canonical and non-canonical splice site sequences in mammalian genes
Next Generation
TransSeq - Program for assembling transcripts from short reads (RNASeq data)
Search for motifs /promoters/functional motifs/
Regsite - List of Plant Regsite database factors used in TSSP and NSITE-PL programs
FPROM - Human promoter prediction
PATTERN - Search for significant patterns in the set of sequences
TSSP - Plants Pol II promoter region and start of transcription
TSSG - Human PolII promoter region and start of transcription
TSSW - Human PolII promoter region and start of transcription (ONLY for academic usage)
NSITE-PL - Recognition of PLANT regulatory motifs, RegSite DB
NSITEM-PL - Recognition of PLANT regulatory motifs, RegSite DB
nsite - Recognition of Regulatory motifs with statistics
nsiteM - Recognition of Conserved Regulatory motifs
nsiteH - Search for functional motifs conserved in orthologs
POLYAH - Recognition of polyadenilation region
PromH (G) - Find promoter with ortologs
PromH (W) - Find promoter with ortologs (academic usage)
CpGFinder - Find GC-islands
ScanWM-P - Search for weight matrix patterns of plant regulatory sequences
Motif Explorer - Motif & promoter visualization sequences
PlantProm - experimentally verified plant promoters datadase
Analysis of expression data
SELTAG - Analysis of expresion data
Alignment /Sequences&genomes/
FMAP - mapping DNA/protein sequence on genome
SCAN2 - Comparison of 2 genomic sequences (with Java viewer)
SCAN2a - Comparison of 2 aminoacid sequences (with Java viewer)
DBSCAN - Comparing your sequence with Database (with Java viewer)
EST_map - Mapping your mRNA/EST to Chromosome sequence of Human genome
PROT_MAP - Mapping of a set of proteins on genome
Genomes Match - comparison of 2 genomes or chromosomes
Genomes Match 2- new version of comparison of 2 genomes or chromosomes (without viewer)
Genome Match - Java Alignment Browser
MaliP - Multiple alignment for protein sequences
MaliN - Multiple alignment for nucleotide sequences
FoldRNA - RNA secondary structure prediction through energy minimization
BestPal_empirical - Calculates best palindrome for given rna sequence, and also a set suboptimal palindromes (sorted by energy)
BestPal_helix - Calculates best palindrome for given rna sequence with restrictions
BestPal_window - Calculates best palindrome for given rna sequence scanning the sequence with a window (for long sequences)
findMiRNA - programm for search MiRNA
TargetMiRna - Search target for MiRNA
Protein Location /pattern
ProtComp - Predict the subcellular localization for Animal/Fungi
ProtComp - Predict the subcellular localization for Plant
ProtCompB - localization of bacterial proteins
PSITE - Search for Prosite patterns with statistics
CTL-epitope-Finder - Program for prediction of putative cytotoxic T lymphocyte (CTL) epitopes
Protein structure
PSSFinder - Prediction of protein secondary structure using Markov chains.
SSPAL - Nearest-neighbor with local alignments SS prediction
NNSSP - Nearest-neighbor SS prediction
SSP - Segment-oriented SS prediction
SSENVID - Protein secondary structure and environment assignment from atomic coordinates
PDISORDER - Protein Disorder Prediction
GETATOMS - Atomic coordinates using homologous protein
3D-comp - Structure Alignment to Superposition
AbIni3D - Ab inition folding
MDynSB - Program MDynSB is designed to perform multiple tasks with protein structure
HMod3DMM - Energy minimization program by molecular mechanic
CYS_REC - Prediction of SS-bonding States of Cysteines in Protein Sequences
3DmodelFit - Program for comparison protein 3D model and its original structure
Protein/DNA 3D-Visual Works
3D-EXPLORER - Visual works with 3D of a Structure
3D-COMPARSION - Visualization of Compared by CE 2 Structures
3D-match - Comparing 3D structures of two proteins
3D-MatchDB - Find structural alignments by real time search in the PDB database
SeqMan
SeqMan - Manipulations with sequences
SMAP - Mapping oligonucleotides to genome
OLIGS - Compute statistics of oligonucleotide occurrences in a set of sequences
OLIGSR - Compute statistics of oligonucleotide redundant occurrences in a set of sequences
OLIGS2 - Compute more frequently oligonucleotides in 1 set and less frequently oligonucleotides in 2 set