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3'-UTR SIRF -- short interspersed repeat finder
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| A database for identifying clusters of short interspersed repeats in 3' untranslated regions.
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ApE- A Plasmid Editor
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| Edit, annotate and draw plasmid sequences.
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BCM Search Launcher -- Nucleic Acid Search tool
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| Search for similar sequences to a nucleotide sequence from various databases.
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BLAST 2 SEQUENCES
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| Compare two nucleotide or protein sequences using a local alignment algorithm.
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BLAST Filter and GraphAlign -- Rule-based Formation and Analysis of Multiple DNA and Protein Sequences
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| Build and analyze sets of related DNA and protein sequences.
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BLAST against Caenorhabditis elegans / Caenorhabditis briggsae sequences
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| Compare your query sequence to DNA sequence or protein products of Caenorhabditis elegans or Caenorhabditis briggsae
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BLAST against plant genomes
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| Compare your query sequence to DNA sequences mapped in, or associated with, plant genomes.
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BLAST the Drosophila melanogaster / Anopheles gambiae genomes
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| Compare your query sequence to DNA sequence or protein products from Drosophila melanogaster or from Anopheles gambiae genomes.
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BLAST the Fugu genome
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| BLAST your sequence against the Japanese pufferfish, Fugu rubripes ('torafugu'), the smallest known genome among vertebrates.
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BLAST the human genome
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| Compare your query sequence to the working draft sequence of the human genome or its mRNA and protein products.
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BLAST the mouse genome
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| BLAST your sequence against mouse specific sequences.
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BLAT Search Genome
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| Quickly find sequences of 95% and greater similarity of length 40 bases or more for DNA or 80% and greater similarity of length 20 amino acids or more for protein in a genome.
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Batch Blast Extractor -- an automated blastx parser application
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| Extract information from BLAST output.
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Blast The Zebrafish Genome
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| Blast your sequence against zebrafish specific sequences.
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Blast the Rat Genome
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| Blast your sequence against Rat specific sequences.
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Blast the Rat Genome Sequences
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| To blast the rat genome with options to limit the blast against specific chromosomes.
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CENSOR -- repetitive elements identification tool
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| Detect repetitive sequence in a query DNA sequence by screening it against a collection of repeats.
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CHOP -- Visualization of ‘Wobbling’ and Isolation of Highly Conserved Regions from Aligned DNA Sequences
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| Find regions suspected of containing coding sequences and visualize nucleotide diversity between two genomic or gene sequences.
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Cloning vector collection
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| Find cloning vector sequences and maps.
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CorGen -— measuring and generating long-range correlations for DNA sequence analysis
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| Generate random sequences based on measured long-range correlations in the base composition of a given DNA.
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CorreLogo -- an online server for 3D sequence logos of RNA and DNA alignments
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| Generate a three-dimensional representation for a given RNA or DNA sequence alignment. |
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DIALIGN -- Multiple DNA and Protein Sequence Alignment at BiBiServ
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| Align multiple DNA or protein sequences. |
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DINAMelt web server for nucleic acid melting prediction
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| Predict hybridization, folding and melting profiles for two strands of DNA or RNA.
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DNA analysis servers -- plot.it, bend.it, model.it and IS
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| Use a collection of methods to analyze and graphically represent various DNA parameters.
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DNA and Protein Sequence Manipulation Suite 2
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| Conduct a variety of analysis of DNA and protein sequences.
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DNAPlotter -- Circular and linear interactive genome visualisation
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| Generate images of circular and linear DNA maps to display regions and features of interest.
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Do-It-Yourself Sequence Comparison using WU-Blast 2.0
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| Use this blast tool to blast query sequence against your own collection of sequences. |
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EMBOSS Pair wise Alignment
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| Compare two sequences with either local or global alignment algorithms.
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EXPASY Proteome Tools Collection
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| Use a collection of tools for protein analyses. |
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Ensembl Trace Server
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| Provides a permanent archive for single-pass DNA sequencing reads and associated traces and quality values.
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Entrez nucleotide database
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| Retrieve nucleotide sequence from GenBank.
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Expasy -- A DNA Translation Tool
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| Translate a DNA seq to a protein sequence
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FeatureScan -- revealing property-dependent similarity of nucleotide sequences
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| Compare physico-chemical properties of different DNA sequences.
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GATA -- a Graphic Alignment Tool for Comparative Sequence Analysis
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| Conduct exhaustive sequence alignment for comparative analysis of two non-coding DNA sequences.
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GIMSAN -- A Gibbs motif finder with significance analysis
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| A novel tool for de novo motif finding.
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GenDecoder -- genetic code prediction for metazoan mitochondria
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| Predict the genetic code of metazoan mitochondria.
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Kalign, Kalignvu and Mumsa -- web servers for multiple sequence alignment
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| Conduct multiple alignments and subsequent quality evaluation.
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MAK, a computational tool kit for automated MITE analysis
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| Analyze miniature inverted repeat transposable elements (MITEs)in higher eukaryotic genomes.
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MAVL/StickWRLD -- analyzing structural constraints using interpositional dependencies in biomolecular sequence alignments
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| Detect and display both positive and negative inter-positional correlations in nucleic acid and protein sequences.
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Maviant -- multi-purpose alignment viewing and annotation tool
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| Provides DNA chromatogram and alignment views, facilitates evaluation of predictions and supports direct manual annotation.
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MegaBLAST
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| Compare sequences that differ slightly as a result of sequencing errors.
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ModelTest Server -- a web-based tool for the statistical selection of models of nucleotide substitution online
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| Conduct statistical selection of nucleotide substitution models.
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MotifMap -- a human genome-wide map of candidate regulatory motif sites
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| Explore a comprehensive map of regulatory elements in the human genome.
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MotifVoter -- variance based ensemble method for discovery of binding sites
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| A novel ensemble method for fine-grained integration of generic motif finders.
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MultiPipMaker and supporting tools -- alignments and analysis of multiple genomic DNA sequences
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| Align multiple, long genomic DNA sequences quickly and with good sensitivity. |
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NEBcutter -- A restriction analysis tool
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| Find restriction digestion map of a DNA sequence.
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Nucleotide query - Protein db [blastx]
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| Find similar proteins to the translated query in a PROTEIN database.
Blastx compares the translation of the nucleotide query sequence to a protein database
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PACdb -- PolyA Cleavage Site and 3'-UTR Database
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| Search for putative 3'-processing sites and 3'-UTR sequences for multiple model organisms.
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PARALIGN -- rapid and sensitive sequence similarity searches powered by parallel computing technology
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| Identify distantly related sequences in both nucleotide and amino acid sequence databases.
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PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference
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| Calculate maximum likelihood phylogenies from DNA and protein sequences. |
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POWER -- PhylOgenetic WEb Repeater—an integrated and user-optimized framework for biomolecular phylogenetic analysis
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| Perform user-friendly pipeline phylogenetic analysis of protein or DNA sequences.
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PROTOGENE -- turning amino acid alignments into bona fide CDS nucleotide alignments
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| Back translate protein multiple sequence alignments.
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PSD -- Personal Sequence Database
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| A suite of tools to create and maintain web-accessible sequence databases.
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PatMaN -- a DNA pattern matcher for short sequences
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| Rapid alignment of short sequences to large databases.
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PatMatch -- a program for finding patterns in peptide and nucleotide sequences
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| Search for short nucleotide or peptide sequences such as cis-elements in nucleotide sequences or small domains and motifs in protein sequences. |
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PatSearch -- a program for the detection of patterns and structural motifs in nucleotide sequences
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| Search for specific combinations of oligonucleotide consensus sequences, secondary structure elements and position-weight matrices in given DNA sequences.
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Phylemon -- A suite of web tools for molecular evolution, phylogenetics and phylogenomics
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| Phylemon is a web server that integrates a selected suite of more than 20 different tools from the most popular stand-alone programs of phylogenetic and evolutionary analysis. |
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PlasMapper -- A web server for drawing and auto-annotating plasmid maps
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| Automatically generates and annotates high-quality circular plasmid maps.
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PlasmID -- a centralized repository for plasmid clone information and distribution
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| Search for annotated information on plasmids and vectors from this comprehensive plasmid repository
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RE-MuSiC: A Tool for Multiple Sequence Alignment with Regular Expression Constraints
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| Construct a multiple sequence alignment by incorporating biological knowledge of sequences (such as motifs, patterns, signatures or fingerprints) into the alignment procedure. |
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REPK -- An analytical web server to select restriction endonucleases for terminal restriction fragment length polymorphism analysis
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| Maximize your ability to discriminate terminal restriction fragments obtained during T-RFLP to take advantage of this powerful community fingerprinting technique. |
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ReadSeq
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| Converts DNA or protein sequence input into various file formats.
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Refseq -- a curated non-redundant sequence database of genomes, transcripts and proteins
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| Retrieve curated, non-redundant reference mRNA sequences from NCBI.
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Repbase Update -- a database of eukaryotic repetitive elements
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| Search for repetitive elements from diverse eukaryotic organisms.
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RepeatMasker
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| Identify and mask repeats in DNA sequences.
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Restriction Site Analysis Tool -- tacg V4.1
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| Find restriction digestion map of a DNA sequence and create a GCG like ladder map.
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RevTrans -- multiple alignment of coding DNA from aligned amino acid sequences
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| Take a set of DNA sequences, virtually translate them, align the peptide sequences, and use this as a scaffold for constructing the corresponding DNA multiple alignments.
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SCOPE -- Suite for Computational identification Of Promoter Elements
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| A web server for practical de novo motif discovery.
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SERpredict -- Specific Exonized Retroelement prediction
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| Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements.
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SIC -- a tool to detect short inverted segments in a biological sequence
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| Search short inverted segments (length 3 Bp to 5000 Bp) in a DNA sequence.
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SIRW -- a web server for the Simple Indexing and Retrieval System that combines sequence motif searches with keyword searches
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| Search protein/nucleotide databases with keywords and a sequence motif.
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SOAP -- short oligonucleotide alignment program
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| A program for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences.
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SPA -- simple web tool to assess statistical significance of DNA patterns
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| Compute DNA sequence pattern occurrences p-value on text.
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STAMP: a web tool for exploring DNA-binding motif similarities.
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| Search DNA motifs against databases of known motifs (JASPAR, TRANSFAC etc.)
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Similarity Searching by FASTA
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| Conduct sequence similarity searching against complete proteome or genome databases using the Fasta programs.
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Standard nucleotide-nucleotide BLAST
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| Find similar sequences to a query sequence from the Genbank nucleotide databases
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Stitchprofiles.uio.no -- analysis of partly melted DNA conformations using stitch profiles
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| Perform computations on DNA melting, thus predict the localized separation of the two strands for DNA sequences.
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Swelfe -- a detector of internal repeats in sequences and structures
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| A tool to detect internal repeats in DNA and amino acid sequences and in 3D structures.
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Swiss EMBnet node web server
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| Use a collection of bioinformatics tools at this portal site.
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TRACTS -- a program to map oligopurine.oligopyrimidine and other binary DNA tracts
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| Map the locations and frequencies of DNA tracts composed of only two bases.
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TRDB — The Tandem Repeats Database
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| Search for various information and analyze repeats in genomic DNA.
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Tcoffee@igs -- A web server for computing, evaluating and combining multiple sequence alignments
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| Conduct and evaluate multiple sequence alignments for protein, DNA and RNA. |
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The Gibbs Centroid Sampler
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| Locate conserved elements in biopolymer sequences.
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VectorNTI Suite Version 10 (free to nonprofit users)
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| Design and analyze primers for different types of PCR-based amplifications. |
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ViroBLAST -- a stand-alone BLAST web interface for nucleotide and amino acid sequence similarity searches
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| Query multiple databases and user's datasets.
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Virtual Ribosome -- a comprehensive DNA translation tool with support for integration of sequence feature annotation
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| Use this comprehensive tool for translating DNA sequences to the corresponding peptide sequences.
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WAViS -- Tools for Handling, Visualization and Presentation of Multiple DNA/protein sequence Alignments
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| Prepare publication-quality pictures of DNA or protein multiple sequence alignments.
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WatCut -- An on-line tool for restriction analysis, silent mutation analysis, and SNP analysis
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| Perform oligo sequence silent mutation analysis, restriction analysis, and
scanning for amplification-created restriction sites for the detection of single nucleotide polymorphisms.
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WebCutter 2.0 - A restriction mapping tool
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| Find restriction digestion map of a DNA sequence and also find sites which may be introduced by silent mutagenesis.
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WebMOTIFS -- an online tool for motif discovery, scoring, analysis, and visualization
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| Automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches.
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WebTraceMiner -- a web service for processing and mining EST sequence trace files
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| A public sequence processing service for raw EST traces.
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YASS -- enhancing the sensitivity of DNA similarity search
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| Perform DNA local alignment of genomic sequences in FASTA or plain format.
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ZiFiT -- Zinc Finger Targeter
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| An engineered zinc finger/target site design tool.
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eProbalign: generation and manipulation of multiple sequence alignments using partition function posterior probabilities
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| Compute multiple sequence alignments from partition function posterior probabilities. |
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enoLOGOS -- a versatile web tool for energy normalized sequence logos
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| Generate sequence logos from DNA and protein sequences. |
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mreps -- efficient and flexible detection of tandem repeats in DNA
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| Identify serial repeats (tandem repeats) in DNA sequences.
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