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The ISREC Group Servers The ISREC Group Servers
The ISREC Group Servers- Detection and assessment of similarity between distantly related sequences by means of a variety of remotely-executable software - from the Swiss Inst. for Experimental Cancer Research. ...
Sequence Alignment and Modeling System Sequence Alignment and Modeling System
Sequence Alignment and Modeling System- Implementation of hidden Markov models for sequence analysis. Free UNIX software for nonprofit groups, and sequences can be submitted online. ...
REBASE REBASE
REBASE- The restriction enzyme database. Maintained by the New England Biolabs, USA. ...
WatCut WatCut
WatCut- Provides restriction analysis, silent mutation scanning and SNP-RFLP analysis. Allows for utilization of all commercially available type II restriction enzymes. ...
RestrictionMapper RestrictionMapper
RestrictionMapper- Finds restriction enzyme cleavage sites in linear and circular DNA sequences. Provides also a virtual digest function. ...
Graphical Codon Usage Analyzer Graphical Codon Usage Analyzer
Graphical Codon Usage Analyzer- Displays the codon quality in two different ways, codon usage frequency or relative adaptiveness values. FAQ included. ...
PlasMapper PlasMapper
PlasMapper- Offers server generated plasmid maps and image files, from input DNA sequences up to 20,000 bp. Includes citation, and downloadable source code. Maintained by the University of Alberta, USA. ...
NEBcutter NEBcutter
NEBcutter- Provides a DNA sequence analysis to find restriction enzymes sites. Finds also non-overlapping open reading frames using the E.coli genetic code. ...
Readseq Readseq
Readseq- Converts amino acid and nucleotide sequence data formats including FASTA, GenBank, Phylip and others. Maintained by NIH, USA. ...
Oligo Calc: Oligonucleotide Properties Calculator Oligo Calc: Oligonucleotide Properties Calculator
Oligo Calc: Oligonucleotide Properties Calculator- Provides reverse complement sequence for DNA or RNA primer strands, self complementarity check, physical and thermodynamic constants, melting temperature (Tm). Includes ...
Primer-BLAST Primer-BLAST
Primer-BLAST- Provides primers specific to the PCR template sequence. Includes primer pair specificity checking against a selected database. ...
StarORF StarORF
StarORF- A Java application that facilitates the identification of potential ORFs, based on provided DNA sequence and probable ORF length. ...
BlueGnome BlueGnome
BlueGnome- Application of advanced statistical methods to the information bottlenecks in drug discovery. ...
ORF Finder ORF Finder
ORF Finder- Identifies all ORFs using the standard or alternative genetic codes. Provides an interactive, graphical interface and allow for saving of a deduced amino acid sequence in various formats. Allows searching aga ...
REBsites REBsites
REBsites- Provides restriction enzyme digest analysis of the input DNA sequence. Results are presented graphically as a "virtual gel". ...
TACG TACG
TACG- DNA restriction enzyme analysis. Provides a number of hits per enzyme and a list of non-cutters. Allows for selection of the enzymes and parameters. ...
Silent Silent
Silent- Silent mutation restriction enzyme scan. Finds new restriction sites to insert (mutate) with no translation change. ...
RaCC: Rare Codon Calculator RaCC: Rare Codon Calculator
RaCC: Rare Codon Calculator- Determines the number and highlights a rare E. coli codons in a provided DNA sequence. Maintained by UCLA, USA. ...
Rare Codon Analysis Rare Codon Analysis
Rare Codon Analysis- Provides graphical and numerical representation of the codon adaptation index, frequency distribution and GC content of the DNA sequence. Maintained by the GenScript, USA. ...
SplitsTree 2 SplitsTree 2
SplitsTree 2- Tool that uses split decomposition method to analyze and visualize distance data from biological sequences. ...
Vista tools Vista tools
Vista tools- Multiple sequence alignment server and whole genome alignment database. ...
MultAlign MultAlign
MultAlign- A multiple-sequence alignment program that also includes distance matrix methods for inferring trees. ...
TreeGen TreeGen
TreeGen- Tree generation from distance data. [Results by email] ...
JAligner JAligner
JAligner- Open source Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment. ...
SWISS-PROT + TrEMBL SWISS-PROT + TrEMBL
SWISS-PROT + TrEMBL- The SWISS-PROT database contains high-quality annotation, is non-redundant and cross-referenced to many other databases. SWISS-PROT is accompanied by TrEMBL, a computer-annotated supplement, which co ...
Protein Information Resource Protein Information Resource
Protein Information Resource- PIR is a non-redundant annotated protein sequence database, and analytical tools, maintained by collaboration of MIPS, in Munich and the Japanese International Protein Sequence Database (JIP ...
InterPro InterPro
InterPro- A database built from Pfam, PRINTS and PROSITE. ...
Munich Information Center for Protein Sequences (MIPS) Munich Information Center for Protein Sequences (MIPS)
Munich Information Center for Protein Sequences (MIPS)- Bioinformatics research group offering organism specific information (Yeast, Cress) as well as search tools for public databases. ...
Molecular Biology Tools Online Molecular Biology Tools Online
Molecular Biology Tools Online- Includes WebOligoMelt (Annealing temperature of oligonucleotides), Virtual Ribosome (translate nucleotide sequences into peptides), and SeqScanGraph (graph melting temperature along nucleo ...
ProtFun ProtFun
ProtFun- Ab initio predictions of protein function from protein sequence. The method works by integrating various predicted post-translational and localizational aspects of the proteins submitted. ...
3D-PSSM Fold Recognition 3D-PSSM Fold Recognition
3D-PSSM Fold Recognition- Combines sequence and structural information for predicting the structure and/or function of your protein sequence, and can detect remote homologies beyond PSI-Blast. ...
Protein Structure Prediction Server (PSIPRED) Protein Structure Prediction Server (PSIPRED)
Protein Structure Prediction Server (PSIPRED)- 3D protein structure prediction from amino acid sequence. Includes MEMSAT for transmembrane topology prediction, GenTHREADER and mGenTHREADER for fold recognition. ...
Jpred Jpred
Jpred- Secondary protein structure prediction from amino acid sequence; based on a consensus from several methods including DSC, PHD, NNSSP, PREDATOR, ZPRED, and MULPRED. ...
Proteomics Tools Proteomics Tools
Proteomics Tools- Online software for protein analysis from the Swiss Institute of Bioinformatics (SIB). ...
Melanie II 2-D Analysis Software Melanie II 2-D Analysis Software
Melanie II 2-D Analysis Software- Powerful, state-of-the-art, 2-D analysis software package with user-friendly interface from the Swiss Institute of Bioinformatics. ...
UniProt UniProt
UniProt- UniProt (Universal Protein Resource) is a catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and P ...
ConSurf ConSurf
ConSurf- Identifies functionally important regions on the surface of a protein or domain, of known three-dimensional (3D) structure using the phylogenetic relations between close sequence homologues. ...
MultiProt MultiProt
MultiProt- Service for detecting the multiple structural alignments of proteins. Uses the common geometrical cores between the input molecules. Does not require that all the input molecules participate in the alignment. ...
ESyPred3D ESyPred3D
ESyPred3D- ESyPred3D is an automated homology modeling program getting benefit of the increased alignment performances of a new alignment strategy using neural networks. The final three dimensional structure is built usi ...
PFP: Automated Function Prediction Server PFP: Automated Function Prediction Server
PFP: Automated Function Prediction Server- Accepts a single query protein sequence and returns the most probable Gene Ontology functional annotations in each of the three ontologies. ...
Critical Outcome Technologies Critical Outcome Technologies
Critical Outcome Technologies- Offers in silico drug discovery service to the pharmaceutical industry. Based in London, Ontario. ...
ELM - Functional Sites in Proteins ELM - Functional Sites in Proteins
ELM - Functional Sites in Proteins- Predicts functional sites (linear motifs) in proteins, such as post-translational modification sites, ligand motifs, and targeting signals. Context-based rules and logical filters are ...
Phyre- Protein Homology/analogY Recognition Engine Phyre- Protein Homology/analogY Recognition Engine
Phyre- Protein Homology/analogY Recognition Engine- Phyre is a free for academics service for predicting the 3-dimensional structure of a protein amino acid sequence. ...
SSM SSM
SSM- Provides interactive service for matching protein structures in 3D and looking for structural homologues in PDB and SCOP databases, as well as in user-uploaded sets of structures. ...
TRANSFAC-The Transcription Factor Database TRANSFAC-The Transcription Factor Database
TRANSFAC-The Transcription Factor Database- A compilation of transcriptional regulatory protein factors and their cognate gene promoter elements along with DNA sequence search and analysis programs - from GBF, Braunschwe ...
MODBASE MODBASE
MODBASE- A database of annotated comparative protein structure models. The database includes fold assignments and alignments as well as information about putative ligand binding sites, SNP annotation, and protein-protein ...
DisEMBL DisEMBL
DisEMBL- Computational tool for sequence based prediction of intrinsic protein disorder and unstructured regions within a protein. ...
TopMatch: Protein Structure Comparison TopMatch: Protein Structure Comparison
TopMatch: Protein Structure Comparison- Public web service for the alignment and superposition of protein structures and the instant visualization of structural similarities. ...
The ProCKSI Server The ProCKSI Server
The ProCKSI Server- A decision support system for protein structure comparison. It provides tools for visualising, analysing, clustering and comparing results. ...
Isoelectric Point Estimator Isoelectric Point Estimator
Isoelectric Point Estimator- Calculator with graphical user interface written in Qt library. ...

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