| RepeatMasker |
Masking repeats and low complexity DNA sequences. |
| Censor |
CENSOR - a program for identification and elimination of repetitive
elements from DNA sequences. |
| Procrustes |
PROCRUSTES: Gene Recognition via Spliced Alignment |
| CodonW |
Codonw: Correspondence Analysis of Codon Usage |
| C.U.D. |
Codon Usage Database |
| S.M.S. |
The Sequence Manipulation Suite for analyzing and formatting DNA and
protein sequences. |
| Promoter Scan |
Predicts Promoter regions based on scoring homologies with putative
eukaryotic Pol II promoter sequences. |
| Promoter 2.0 |
Promoter 2.0 predicts transcription start sites of vertebrate PolII
promoters in DNA sequences |
| NetStart 1.0 |
The NetStart server produces neural network predictions of translation
start in vertebrate and Arabidopsis thaliana nucleotide sequences |
| AUG |
AUG_EVALUATOR for start codons prediction |
| CpG Plot |
Detection of regions of genomic sequences that are rich in the CpG
pattern |
| GeneMark |
GeneMark. A family of gene prediction programs |
| GeneMark (EBI) |
GeneMark at EBI. |
| ORF Finder |
ORF Finder (Open Reading Frame Finder) |
| FramePlot |
Predicts protein-coding region of high G+C content bacterial DNA, such
as Streptomyces |
| Glimmer |
Glimmer uses interpolated Markov models (IMMs) to identify coding
regions. |
| GENSCAN |
Identification of complete gene structures in genomic DNA |
| NetGENE |
The NetGene2 server is a service producing neural network predictions
of splice sites in human, C. elegans and A. thaliana DNA. |
| HMMgene |
HMMgene: Prediction of vertebrate and C. elegans genes. |
| MZEF |
MZEF is an internal coding exon prediction program |
| Genie |
Genie: Gene Finder Based on Generalized Hidden Markov Models in Drosophila |
| GeneId |
GeneId is a program to predict genes in anonymous genomic sequences
designed with a hierarchical structure. (Roderic Guigo's Lab). |
| GlimmerM |
A gene finder derived from Glimmer, but developed specifically for
eukaryotes. |
| MetaGene Server |
MetaGene 2.7 is a powerful tool designed to provide exhaustive analysis
of predicted gene features in sequence. |
| Webgene |
Webgene: tools for prediction and analysis of protein-coding gene structure. |
| ClustalW_EMBL |
CLUSTAL W (1.75) Multiple Sequence Alignments (EMBL-ES) |
| ClustalW_EBI |
ClustalW Server at EBI |
| ClustalW_BioWeb |
ClustalW Server at the Institut Pasteur (France) |
| T-COFFEE |
T-Coffee: Accurate, but slow, Multiple Sequence Alignment server (EMBNET.CH)
(limit: 30 seq, 1000 res) |
| T-COFFEE |
T-Coffee: Cedric Notredame page (Wageningen Bioinformatics Webportal,
NL) (limit: 20 seq 300 res) |
| CMBI_Tree_Plot |
CMBI Phylogenetic Tree Plot Server (University of Nijmegen, NL) (GIF,
PS,.. trees) |
| Phylodendron |
Phylodendron: Phylogenetic tree printer (EMBL-ES) |
| PHYLIP |
PHYLIP is a free package of programs for inferring phylogenies (Whasington
Univ.) |
| BioWebPHILIP |
PHILIP (web version) at the Institut Pasteur (France) |
| PAUP |
PAUP is a software package for inference of evolutionary trees (Florida
Stat. Univ.) |
| Philogeny
Programs |
Here are some 193 of the phylogeny packages, and 16 free servers. |
| Phylogeny Course |
Molecular Systematics and Evolution Course (London - Rio de Janeiro) |
| MotifScan |
Prosite & Pfam Motif Scan Server (ISREC, CH) |
| ProDom |
ProDom protein domain database (INRA, FR) |
| InterPro |
Integrated resource of protein domains and functional sites. (EBI,
UK) |
| PFAM |
Protein families database of alignments and HMMs (Sanger, UK) |
| CDART |
Conserved Domain Architecture Retrieval Tool (It shows similar
domain achitectures, too) (NCBI) |
| PRINTS |
Protein Motif Fingerprint Database (UCL, UK) |
| SMART |
Simple Modular Architecture Research Tool. Domains/motif detection
(EMBL) |
| SignalP |
Predicts the presence and location of signal peptide (CBS, DK) |
| TMHMM |
Prediction of transmembrane helices in proteins (CBS, DK) |
| HMMTOP |
Prediction of transmembrane helices and topology of proteins (Inst.
Enzymol. Budapest) |
| SignalP |
Predicts the presence and location of signal peptide (CBS, DK) |
| COILS |
Prediction of Coiled Coil Regions in Proteins (ISREC, CH) |
| MultiCoil |
Program for Predicting Two- and Three-Stranded Coiled Coils (MIT, USA) |
| Jpred |
A consensus method for protein secondary structure prediction (EBI,
UK) |
| Psi-Pred |
Protein structure prediction server (secondary structure &
transmembrane topology) (University College London, UK) |
| APSSP |
APSSP: Advanced Protein Secondary Structure Prediction Server (Chandigarh,
INDIA) |
| TOPS |
Topology of Protein Structure (Univ. of Leeds) |
| SAM-T02 |
SAM-T02 secondary structure prediction. |
| Swiss-Model |
SWISS-MODEL. An Automated Comparative Protein Modelling Server (ExPASy,
CH) |
| SWISS-MODEL
Repository |
SWISS-MODEL Repository. A database for theoretical protein models (ExPASy,
CH) |
| WHATIF |
WHAT IF Web interface: homology modelling, drug docking,
electrostatics calculations, structure validation and visualisation. |
| TITO/Modeller |
Modeller at the CBS Bioinformatic Tools Server (Montpellier, France) |
| CPHmodels |
The CPHmodels Server using comparative (homology) modelling (BioCentrum,
Denmark) |
| 3D-JIGSAW |
Automated system to build three-dimensional models for proteins. (Cancer
Research UK) |
| Loops Database |
Protein Loop Classification. (Cancer Research UK). |
| PredictProtein |
The PredictProtein server (TOPITS) (Columbia, USA) |
| PredictProtein
(CNB) |
The PredictProtein server (TOPITS) (EMBnet / CNB, ES) |
| 3D-PSSM/Phyre |
3D-PSSM & Phyre Protein Fold Recognition (Threading) Server (Imperial
Cancer Res. Fund., UK) |
| UCLA-DOE |
UCLA-DOE Fold-Recognition server (UCLA, USA) |
| Psi-Pred (GenThreader) |
Protein structure prediction server (sequence profile based fold
recognition) (University College London UK) |
| SAM-T02 |
SAM-T02 protein structure HMM library search. |
| FFAS |
Fold & Function Assignment System. (Burnham Institute, USA) |
| FUGUE |
FUGUE Profile Library Search Against HOMSTRAD (Cambridge, UK) |
| Threading
Meta-Server |
Threading Meta-Server at the CBS Bioinformatic Tools Server (Montpellier,
France) |
| LOOPP |
A program for potential optimization and alignments (Cornell, USA) |
| Superfamily |
HMM library and genome assignments server (Cambridge, UK) |
| PDB - RCSB |
Protein Data Bank (RCSB) |
| PDBsum |
Summaries and structural analyses of PDB data files (UCL, UK) |
| Get ExPDB |
Get ExPDB entries for a PDB code (Swiss-Model, ExPASy, CH) |
| OCA |
PDB advanced browser(EBI) |
| EC->PDB |
Enzyme Structures deposited in PDB (EBI, UK) |
| Prosite->PDB |
PROSITE patterns in PDB entries (EBI, UK) |
| Ligands->PDB |
List of ligands bound to PDB srtuctures (EBI, UK) |
| RELIBASE |
Relibase: A program for searching protein-ligand databases. |
| NDB |
The Nucleic Acid Database Project (UK) (Nucleic Acid Structures) |
| IMB Jena |
IMB Jena Image Library of Biological Macromolecules (Jena, Germany) |
