Other Analytical Tools HOME Comparison & Alignments Functional Analysis Structural Analysis Other Analytical Tools
ACEDB: A C.Elegans Data Base A software tool to manage and provide easy access to large collections of genomic data.
BCM Search Launcher An on-going project to organize molecular biology-related search and analysis services available on the WWW by function by providing a single point-of-entry for related searches.
BCM ReadSeq Allows to convert Sequence Formats using ReadSeq method
BIMAS: Bioinformatics & Molecular Analysis Section The BIMAS provides guidance, support and resources to scientists throughout the NIH in the genomic and genetic analysis fields of BioInformatics.
BIOLOGY WORKBENCH Database searching integrated with access to a wide variety of analysis and modeling tools, all within a point and click interface that eliminates file format compatibility problems.
Biotoolkit Hundreds of advanced online tools for molecular biology data retrieval, analysis, and visualization. Also provides annotated links to web tools for the study of nucleic acid, genome, and protein structure.
CBRG: Computational Biochemistry Research GroupThis server offers many free and helpful services and tools for Computational Biologists, Biochemists, and Molecular Evolutionists.
CBS_distanceP The server predicts distance constraints between amino acids in proteins from the amino acid sequence.
Comparative Sequence Analysis Here you can test your DNA sequence for sequencing errors.
CUBIC Columbia University Bioinformatics center services PredictProtein, META, PredictNLS, and EVA.
DARWIN: Data Analysis and Retrieval With Indexed Nucleotide/Peptide Sequences An interactive tool for peptide and nucleotide sequence analysis. A growing library of functions for sequence management and analysis, statistics, numerics, graphics, parallel execution and more.
DAS: Transmembrane Prediction Server Predicts transmembrane regions of a query sequence. A number of algorithms designed to identify putative transmembrane helices in the primary amino acid sequence have been developed, and current methods can identify around 90-95% of all true transmembrane segments with an over-prediction rate of only a few percent.
Divide-and-Conquer Multiple Sequence Alignment A program for producing fast, high quality simultaneous multiple sequence alignments of amino acid, RNA, or DNA sequences.
DNA Primer Melt Calculator A handy calculator of PCR primers for DNA Transformation in a nice justified layout of the sequence with codon numbering.
DOGS: Database Of Genome Sizes The purpose of this database is to provide a comprehensive list of estimated genome sizes for different organisms.
Dr. Tsong-Li Wang’s Web Page A collection od sequence analysis tool
Electronic PCR PCR-based sequence tagged sites (STSs) have been used as landmarks for construction of various types of genomic maps. Using "electronic PCR" (e-PCR), these sites can be detected in DNA sequences, potentially allowing their map locations to be determined.
Embl_Amino Acid Analysis Server A server for protein and amino acid analysis.
EMBOSS "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages.
EMBOSS Sequence Analysis Servers A suite of free software tools for sequence analysis, including that of GCG. There are a wide variety of programs that make up the suite, ranging in application from database searching to presentation of sequence data.
ExPASy Proteomics Tools Provides tools from the ExPASy server as well as a few other servers.
ExPASy: Expert Protein Analysis System This server is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE.
ExPASy_3Dcrunch The aim of 3Dcrunch is to submit all entries of the SWISS-PROT and trEMBL databases to SWISS-MODEL. Furthermore, all sequences of bacterial origin will be submitted to fold the recognition algorithm implemented in FoldFit. Taken together, these approaches will yield structural models for all sequences with clear similarities to proteins of know 3-D structure and a suggested fold class for all bacterial sequences.
FASTA Programs at the University of Virginia This web page provides a table of FASTA programs at the University of Virginia.
Gcg: Genetics Computer Group It enables scientists to analyze DNA and protein sequences by editing, mapping, comparing, and aligning them. Other programs facilitate RNA secondary structure prediction, DNA fragment assembly, and evolutionary analysis. GCG serves molecular biologists by building practical tools that implement the most important techniques of mathematical biology.
GenefisherAn interactive PCR primer design program that will process aligned or unaligned sequences.
GENEMARK GeneMark, gene prediction algorithm, has been used for the analysis of EST sequences as well as for predicting rather long exons and designing RT-PCR primers.
Genetic Code Viewer Genetic Code Viewer is a simple tool for showing different versions of genetic code used by various taxonomic groups.
GenomeAtlas The DNA Structural Atlas is a method of visualizing structural features within large regions of DNA. It was originally designed for analysis of complete genomes, but can also be used quite readily for analysis of regions of DNA as small as a few thousand bp in length.
Jambw: Java-based Molecular Biology Workbench The programs and documentation have been put together in order to try to give a free access to the exploitment of the most common bioinformatics operations that a molecular biologist currently has.
LabOnWeb Life science research engine. A collection of gene discovery tools designed to accelerate work in the lab, improve the quality and accuracy of experiments, simplify the delivery of information and help researchers make more informed decisions throughout the discovery process.
Large Dot Plots This page accesses a very fast dot plot algorithm designed for large DNA sequences.
MODELLER MODELLER is most frequently used for homology or comparative modeling of protein three-dimensional structure: the user provides an alignment of a sequence to be modeled with known related structures and MODELLER will automatically calculate a full-atom model. More generally, MODELLER models protein 3D structure by satisfaction of spatial restraints.
Nps@: Network Protein Sequence @nalysis An interactive web server dedicated to protein sequence analysis and available for the biologist community.
PATSCAN A pattern matcher, which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern, which you input.
PCR_Primer Selection This page provides an interface to a PCR primer selection program based on xprimer.
PEDANT: Protein Extraction, Description, and Analysis Tool A software system for completely automatic and exhaustive analysis of protein sequence sets - from individual sequences to complete genomes.
Phylogeny Programs A comprehensive compilation of avaialable phylogeny programs
Primer 3 Designs PCR primers from a nucleotide sequence.
RasMol & Chime: Molecular Visualization Freeware RasMol is free software for looking at molecular structures. Chime shows molecules like RasMol, but unlike RasMol, Chime shows molecules inside a web page.
RDP: Ribosomal Database Project II Provides ribosome related data services, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences.
ReadSeq (at BCM) Allows to convert Sequence Formats using ReadSeq method
Repeat Finder Finds a repeat in a DNA of protein sequence using BLAST.
Repeatmasker Web Server Repeatmasker screens DNA sequences in fasta format against a library of repetitive elements and returns a masked query sequence ready for database searches as well as a table annotating the masked regions.
RIFLE: Rapid Identification by Fragment Length Evaluation Compares restriction patterns of possibly unknown microorganisms against a database of theoretical restriction patterns generated from a 16S rDNA database. Restriction patterns of multiple restriction enzymes can be combined to improve the quality of identification, additional parameters allow the individual adaptation to laboratory processes.
RNA Movies A system for the visualization of RNA secondary structure spaces. Its input is a script consisting of primary and secondary structure information. From this script, the system generates animated graphical structure representations.
ROSE: Random-model Of Sequence Evolution Rose implements a new probabilistic model of the evolution of RNA, DNA, or protein-like sequences. The data created by Rose are suitable for the evaluation of methods in multiple sequence alignment computation and the prediction of phylogenetic relationships.
SBASE A protein domain library sequences that contains 237.937 annotated structural, functional, ligand-binding and topogenic segments of proteins, cross-referenced to all major sequence databases and sequence pattern collections.
SOM-BLOCK A method based on self-organizing maps (SOMs) to find patterns in protein sequences.
SRPDB: Signal Recognition Particle Database Provides Aligned, Annotated and Phylogenetically Ordered Sequences Related to Structure and Function of SRP.
TESS: Transcription Element Search System Searches a nucleic acid sequence for potential transcription factor binding sites from the Transfac database.
The Bio-Web Tools A comprehensive list of Sequence analysis tools.
The Gene Discovery Page If your sequence analysis needs are basic, you are invited to use The Gene Discovery Page for your Bioinformatics solutions. The Gene Discovery Page organizes select web-accessible bioinformatics tools in a coherent fashion.
The Genome Channel A tool for the comprehensive sequence-based view of genomes.
TRADAT: TRAnscription Databases and Analysis Tools Databases that collect experimental relevant data such as TRANSFAC and EPD provide the basis for sequence analysis.
Virtual Genome Center This website provides several bioinformatics tools ranging from database searches to a variety of sequence analysis tools.
Webcutter A tool to help restriction map nucleotide sequences. In addition to restriction site mapping, Webcutter 2 also performs degenerate digests, including the option of finding restriction sites that can be introduced into a sequence by silent mutagenesis ("silent cutters").

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