| GeneBuilder
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Gene Structure Prediction System. Detects exons, TATA boxes, splices sites and poly-A sites.
Submitted Oct 15, 2000
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| MatInspector V2.2
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A form that searches for potential binding sites.
Submitted Sep 04, 2000
Updated Oct 09, 2000
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| Clustalw
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Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
Submitted Sep 04, 2000
Updated Sep 20, 2000
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| Do-It-Yourself
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Do-It-Yourself Sequence Comparison using WU-Blast 2.0
Submitted Sep 04, 2000
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| FASTA
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Performs FastA Sequence Comparison algorithm at the University of Virginia.
Submitted Sep 04, 2000
Updated Oct 09, 2000
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| Repeat Finder
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Locates repeat regions within your sequence.
Submitted Sep 05, 2000
Updated Oct 09, 2000
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| ExPASy - Translate tool
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Translate is a tool which allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence.
Submitted Sep 04, 2000
Updated Oct 17, 2000
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| Geneid WEB Server
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Geneid server is the web server to geneid, a program to predict genes, exons, splice sites and other signals along a DNA sequence.
Submitted Oct 15, 2000
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| Mutability
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A program which takes a DNA sequence and determines how many single point mutations would result in nonsense, missense, or neutral mutations.
Submitted Sep 09, 2000
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| Promoter 2.0
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Promoter2.0 is a program for predicting transcription start sites of vertebrate PolII promoters in DNA sequences. It has been developed as an evolution of simulated transcription factors that interact with sequences in promoter regions. It builds on principles that are common to neural networks and genetics algorithms.
Submitted Dec 09, 2000
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| TESS
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An on-line software for locating and displaying transcription factor binding sites within DNA sequences.
Submitted Nov 05, 2000
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| The Exon-Intron Database
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An exhaustive database of protein-coding intron-containing genes.
Submitted Dec 02, 2000
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| C. elegans ACEDB database
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This is a simple front end for accessing the C. elegans ACEDB database.
Submitted Nov 19, 2000
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| DIALIGN
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DIALIGN is a novel program for multiple alignment developed by Burkhard Morgenstern et al. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing whole segments of the sequences. No gap penalty is used. This approach is especially efficient where sequences are not globally related but share only local similarities, as is the case with genomic DNA and with many protein families.
Submitted Dec 03, 2000
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| ExPASy - Tools
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This page contains some ExPsay tools for protein analysis.
Submitted Sep 04, 2000
Updated Nov 05, 2000
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| GeneMark
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This program is used for gene prediction in genome sequences. Identifies ORFs, exons, and introns.
Submitted Oct 15, 2000
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| Genetic Code Viewer
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Shows Codon Tables for a number of different species including, vertebrate, invertebrate, yeast, mold and more.
Submitted Sep 04, 2000
Updated Sep 20, 2000
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| HCpolya
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Hamming Clustering poly-A prediction in Eukaryotic Genes.
Submitted Oct 15, 2000
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| IMAGE Translate
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Use this page to translate your IMAGE IDs into their corresponding CLONE NAMES. Simply enter your IMAGE IDs in the boxes, and click on FIND CLONE NAMES.
Submitted Dec 04, 2000
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| LALIGN
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Calculates the N-best local alignments.
Submitted Sep 04, 2000
Updated Oct 09, 2000
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| MultAlin
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Multiple sequence alignment by Florence Corpet.
Submitted Sep 04, 2000
Updated Oct 20, 2000
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| NuclPepSearch
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Filling and submitting the following form will search SwissProt for a given nucleotide sequence by running the dynamic programming algorithm by Knecht and Gonnet.
Submitted Sep 04, 2000
Updated Sep 20, 2000
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| QBLAST
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The NCBI is introducing the new QBLAST system that allows users to retrieve results at their convenience and format their results multiple times with different formatting options.
Submitted Sep 04, 2000
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| Reputer
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The REPuter program family provides state of the art software solutions to compute and visualize repeats in whole genomes or chromosomes. This website provides a limited functionality of REPuter, due to our limited server capacities. However it should be useful for sequences up to 100000 bases.
Submitted Dec 02, 2000
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| Signaling PAthway Database
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The Signaling PAthway Database (SPAD) is an integrated database for genetic information and signal transduction systems.
Submitted Nov 19, 2000
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| UniGene
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UniGene is an experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters. Each UniGene cluster contains sequences that represent a unique gene, as well as related information such as the tissue types in which the gene has been expressed and map location.
Submitted Nov 19, 2000
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| YinOYang
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The YinOYang WWW server produces neural network predictions for O-ß-GlcNAc attachment sites in eukaryotic protein sequences.
Submitted Dec 09, 2000
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| Anatomical Dictionary Browser
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Search for mouse anatomical structures and associated expression assay results.
Submitted Nov 19, 2000
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| BioCarta
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Extensive collection of graphic pathways showing molecular and cellular interactions all hyperlinked to specific molecular information and related pathways.
Submitted Sep 04, 2000
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| Codontree
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This program is able to determine a codon usage table for a set of protein coding genes, gene relationship on the basis of codon usage similarity, and compositional features of protein coding genes.
Submitted Sep 05, 2000
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| Completed genomes search and analysis
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BLAST and keyword searches of the functional annotation of the completed genome databases. Search includes BMERC ID, as well as the Genbank PID and EMBL ID when known.
Submitted Oct 17, 2000
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| DBGET Database Links Diagram
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DBGET/LinkDB handlesexisting molecular biology databases and cross-reference links among them.
Submitted Sep 04, 2000
Updated Oct 09, 2000
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| Distance-P
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The distanceP World Wide Web server predicts distance constraints between amino acids in proteins from the amino acid sequence.
Submitted Dec 09, 2000
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| DOGS
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A list of estimated genome sizes for different organisms.
Submitted Oct 17, 2000
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| EMBL Dali
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The Dali server is a network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank. A multiple alignment of structural neighbours is mailed back to you. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences.
Submitted Sep 26, 2000
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| Ensembl Genome Server
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This site represents the June 15th frozen dataset as analysed by a collaborative group of a laboratories. The freeze datasets are continuing, and are likely to be the main form of the human genome over the next months.
Submitted Nov 10, 2000
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| EuroGeneIndexes WU-Blast2
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Identifies a cluster of ESTs related to the submitted sequence.
Submitted Sep 04, 2000
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| Fasta3
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A database of human genes and that allows to get information regarding polymorphisms in the gene as well as functional information relating to the polymorphism.
Submitted Sep 04, 2000
Updated Dec 09, 2000
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| GAIA
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GAIA is a data analysis and storage system for genomic sequence and its annotation. As a data analysis engine it accepts raw genomic sequence and automatically adds significant annotation. As a data storage system, it incorporates such sequence and annotation into its database along with a record of experimental support for the annotation. It facilitates queries against the data and graphical visualization of the query results.
Submitted Oct 17, 2000
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| Gene Finder
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This page contains software tools designed to predict putative internal protein coding exons in genomic DNA sequences.
Submitted Sep 04, 2000
Updated Oct 09, 2000
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| GeneMap'98
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Current map and search engine for >30,000 human gene loci.
Submitted Oct 27, 2000
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| Genome Survey Sequences Database
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The GSS division contains (but is not limited to) the following types of data: random "single pass read" genome survey sequences, cosmid/BAC/YAC end sequences, exon trapped genomic sequences, Alu PCR sequences.
Submitted Dec 02, 2000
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| Genome-Wide Expression
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Genome-wide expression analysis was used to identify genes affected by the FCP1 CTD-phosphatase.
Submitted Sep 04, 2000
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| GETMaps
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The WWW-site GET Maps (Maps of Genes Expressed in Tissues) contains the chromosomal maps of genes expressed in some selected human tissues.
Submitted Nov 19, 2000
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| GXD Index Query Form
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Search for references to the literature on gene expression in mouse development.
Submitted Nov 19, 2000
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| HOBACGEN - Homologous Bacterial Genes Database
|
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HOBACGEN is a database system that contains all the protein sequences of bacteria organized into families. It allows one to select sets of homologous genes from bacterial species and to visualize multiple alignments and phylogenetic trees. Thus HOBACGEN is particularly useful for comparative genomics, phylogeny and molecular evolution studies on bacteria.
Submitted Nov 24, 2000
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| Hovergen
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Hovergen is a database of homologous vertebrate genes. Hovergen allows you to easily select sets of homologous genes among a given set of vertebrate species. Hovergen corresponds to the nuclear and mitochondrial vertebrate sequences subset of GenBank, with some data corrected, clarified, or completed, notably to address the problem of redundancy. Coding sequences have been classified in gene families. Protein multiple alignments and phylogenetic trees have been calculated for each family.
Submitted Nov 24, 2000
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| Human-Mouse Dysmorphology Database
|
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This application consists of three separate databases of human and mouse malformation syndromes together with a database of mouse/human syntenic regions. The mouse and human malformation databases are linked together through the chromosome synteny database. The purpose of the system is to allow retrieval of syndromes according to detailed phenotypic descriptions and to be able to carry out homology searches for the purpose of gene mapping.
Submitted Dec 03, 2000
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| KEGG
|
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Pathways of interacting molecules and genes.
Submitted Sep 04, 2000
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| LocusLink
|
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LocusLink provides a single query interface to curated sequence and descriptive information about genetic loci. It presents information on official nomenclature, aliases, sequence accessions, phenotypes, EC numbers, MIM numbers, UniGene clusters, homology, map locations, and related web sites.
Submitted Nov 19, 2000
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| MAGI
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The purpose of MAGI is to have a single point where a set of sequences can be entered. They are then aligned using one of several multiple sequence alignment programs available and the user can look at the results sometime later using a range of multiple sequence viewing and analysis programs.
Submitted Sep 26, 2000
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| Match-Box
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The Match-Box software proposes protein sequence alignment tools based on strict statistical criteria. The method circumvents the gap penalty requirement: in the Match-Box method, gaps are the result of the alignment and not a governing parameter of the matching procedure. A reliability score is provided below each aligned position. The Match-Box program is particularly suitable for finding and aligning conserved structural motives, in particular in protein core.
Submitted Sep 04, 2000
Updated Sep 20, 2000
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| MedMiner
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The MedMiner filters will extract and organize relevant sentences in the literature based on a gene, gene-gene or gene-drug query. This tool combines the GeneCards and PubMed search engines with user input and automated server-side scripts in an integrated text filtering system.
Submitted Nov 05, 2000
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| MuStaR
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MuStaR™ is a Locus Specific Database System for maintaining data about allelic variants (mutations), and distributing those data via the World Wide Web.
Submitted Oct 31, 2000
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| NetPhos
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The NetPhos WWW server produces neural network predictions for serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins.
Submitted Dec 09, 2000
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| NetPlantGene
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The NetPlantGene World Wide Web server is a service producing neural network predictions of splice sites in Arabidopsis thaliana DNA.
Submitted Dec 09, 2000
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| NetStart
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The NetStart WWW server produces neural network predictions of translation start in vertebrate and Arabidopsis thaliana nucleotide sequences. NetStart has been trained on cDNA-like sequences and will therefore presumably have better performance for cDNAs and ESTs. We have not tested the performance on genome data which may contain introns adjacent to the start codon.
Submitted Dec 09, 2000
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| Online Mendelian Inheritance in Man
|
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The OMIM gene map presents the cytogenetic map location of disease genes and other expressed genes described in OMIM.
Submitted Dec 03, 2000
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Total Visits: 1
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| ORFGene 2
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Gene structure prediction using information on homologous protein sequence.
Submitted Oct 15, 2000
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| ORNL
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View Genome Sequence and Annotation View Different Annotated Features by Chromosome Gene Model Examples Annotate and Analyze New Genome Sequences.
Submitted Sep 04, 2000
Updated Dec 01, 2000
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| Primer3
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A form for making PCR selections. This tool offers a huge amount of parameters.
Submitted Sep 04, 2000
Updated Apr 30, 2004
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| Proteome & Genome Fasta33
|
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Search completed genomes and proteomes.
Submitted Oct 24, 2000
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| Rat Genome Database
|
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The Rat Genome Database is a collaborative effort between leading research institutions involved in rat genetic and genomic research. Its goal, as stated in RFA: HL-99-013 is the establishment of a Rat Genome Database, to collect, consolidate, and integrate data generated from ongoing rat genetic and genomic research efforts and make these data widely available to the scientific community. A secondary, but critical goal is to provide curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data.
Submitted Nov 19, 2000
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| RATMAP
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The Rat Genome Database: includes Searches, Maps, Homology, Nomenclature and more.
Submitted Nov 19, 2000
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| READSEQ
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Converts input DNA/AA sequence to specified format (Input format is determined automatically).
Submitted Nov 19, 2000
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| Rummage
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This site provides online access to the high throughput sequence annotation software Rummage. To run Rummage remotely you'll need to register, first! Once you are a registered user, you can submit requests for sequence annotations.
Submitted Sep 05, 2000
Updated Oct 09, 2000
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| SAWTED
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SAWTED (Structure Assignment With Text) is a method to improve the coverage of the detection of remote homologues of known structure by sequence searches (e.g. PSI-BLAST) and fold recognition programs.
Submitted Sep 04, 2000
Updated Sep 20, 2000
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| SpliceView
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Splice Prediction using Consensus Sequences.
Submitted Oct 17, 2000
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| The Genome Database
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The official central repository for genomic mapping data resulting from the Human Genome Project.
Submitted Oct 27, 2000
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| TIGR C. elegans Gene Index
|
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The TIGR C. elegans Gene Index integrates research data from international C. elegans EST sequencing and gene research projects. The ultimate goal of the TIGR Gene Index projects, including CeGI, is to represent a non-redundant view of all C. elegans genes and data on their expression patterns, cellular roles, functions, and evolutionary relationships.
Submitted Nov 19, 2000
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| TIGR Drosophila Gene Index
|
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The TIGR Drosophila Gene Index integrates research data from international Drosophila EST sequencing and gene research projects. The ultimate goal of the TIGR Gene Index projects, including DGI, is to represent a non-redundant view of all Drosophila genes and data on their expression patterns, cellular roles, functions, and evolutionary relationships.
Submitted Nov 19, 2000
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| TIGR MOUSE Gene Index
|
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The TIGR Mouse Gene Index (MGI) integrates research data from international mouse gene research projects. All data in the Index are freely available and do not require a user account for access.The goal of this project is to ultimately represent a non-redundant view of all mouse genes and data on their expression patterns, cellular roles, functions, and evolutionary relationships.
Submitted Nov 19, 2000
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| TIGR Rat Gene Index
|
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The TIGR Rat Gene Index (RGI) integrates research data from international rat gene research projects. All data in the Index are freely available and do not require a user account for access.The goal of this project is to ultimately represent a non-redundant view of all rat genes and data on their expression patterns, cellular roles, functions, and evolutionary relationships.
Submitted Nov 19, 2000
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| TMHMM
|
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Prediction of transmembrane helices in proteins.
Submitted Dec 09, 2000
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| Transcription Regulatory Regions Database
|
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TRRD contains information about structural-functional organization of these transcription regulatory regions, protein factors involved in transcription regulation, and transcription signals.
Submitted Nov 19, 2000
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| Transterm
|
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A database of mRNA regions and motifs from all species and genomes. Browse the pre-computed data tables, search the sequence databases or search your own sequences.
Submitted Nov 05, 2000
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| Web Signal Scan Service
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Find and list homologies of published signal sequences with the input DNA sequence.
Submitted Nov 19, 2000
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| WebLogo
|
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This form generates sequence logos. Sequence logos are a graphical way of representing and visualizing biological information. Generally they supercede consensus sequences as more precise and useful ways of conveying data.
Submitted Sep 04, 2000
Updated Sep 20, 2000
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| Wise2
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Compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.
Submitted Oct 15, 2000
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