Web Tools

MatInspector V2.2  
A form that searches for potential binding sites.
Submitted: Sep 04, 2000
Clustalw  
Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
Submitted: Sep 04, 2000
Do-It-Yourself  
Do-It-Yourself Sequence Comparison using WU-Blast 2.0
Submitted: Sep 04, 2000
FASTA  
Performs FastA Sequence Comparison algorithm at the University of Virginia.
Submitted: Sep 04, 2000
Repeat Finder  
Locates repeat regions within your sequence.
Submitted: Sep 05, 2000
ExPASy - Translate tool  
Translate is a tool which allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence.
Submitted: Sep 04, 2000
Geneid WEB Server  
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
Mutability  
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
Promoter 2.0  
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
TESS  
An on-line software for locating and displaying transcription factor binding sites within DNA sequences.
Submitted: Nov 05, 2000
The Exon-Intron Database  
An exhaustive database of protein-coding intron-containing genes.
Submitted: Dec 02, 2000
C. elegans ACEDB database  
This is a simple front end for accessing the C. elegans ACEDB database.
Submitted: Nov 19, 2000
DIALIGN  
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
ExPASy - Tools  
This page contains some ExPsay tools for protein analysis.
Submitted: Sep 04, 2000
GeneMark  
This program is used for gene prediction in genome sequences. Identifies ORFs, exons, and introns.
Submitted: Oct 15, 2000
Genetic Code Viewer  
Shows Codon Tables for a number of different species including, vertebrate, invertebrate, yeast, mold and more.
Submitted: Sep 04, 2000
LALIGN  
Calculates the N-best local alignments.
Submitted: Sep 04, 2000
MultAlin  
Multiple sequence alignment by Florence Corpet.
Submitted: Sep 04, 2000
NuclPepSearch  
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
QBLAST  
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
Reputer  
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
UniGene  
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
YinOYang  
The YinOYang WWW server produces neural network predictions for O-ß-GlcNAc attachment sites in eukaryotic protein sequences.
Submitted: Dec 09, 2000
Anatomical Dictionary Browser  
Search for mouse anatomical structures and associated expression assay results.
Submitted: Nov 19, 2000
BioCarta  
Extensive collection of graphic pathways showing molecular and cellular interactions all hyperlinked to specific molecular information and related pathways.
Submitted: Sep 04, 2000
Completed genomes search and analysis  
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
DBGET Database Links Diagram  
DBGET/LinkDB handlesexisting molecular biology databases and cross-reference links among them.
Submitted: Sep 04, 2000
Distance-P  
The distanceP World Wide Web server predicts distance constraints between amino acids in proteins from the amino acid sequence.
Submitted: Dec 09, 2000
DOGS  
A list of estimated genome sizes for different organisms.
Submitted: Oct 17, 2000
EMBL Dali  
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
Ensembl Genome Server  
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
EuroGeneIndexes WU-Blast2  
Identifies a cluster of ESTs related to the submitted sequence.
Submitted: Sep 04, 2000
Fasta3  
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
GAIA  
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
GeneMap'98  
Current map and search engine for >30,000 human gene loci.
Submitted: Oct 27, 2000
Genome Survey Sequences Database  
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
Genome-Wide Expression  
Genome-wide expression analysis was used to identify genes affected by the FCP1 CTD-phosphatase.
Submitted: Sep 04, 2000
GXD Index Query Form  
Search for references to the literature on gene expression in mouse development.
Submitted: Nov 19, 2000
KEGG  
Pathways of interacting molecules and genes.
Submitted: Sep 04, 2000
LocusLink  
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
Match-Box  
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
MuStaR  
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
NetPhos  
The NetPhos WWW server produces neural network predictions for serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins.
Submitted: Dec 09, 2000
NetPlantGene  
The NetPlantGene World Wide Web server is a service producing neural network predictions of splice sites in Arabidopsis thaliana DNA.
Submitted: Dec 09, 2000
NetStart  
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
Online Mendelian Inheritance in Man  
The OMIM gene map presents the cytogenetic map location of disease genes and other expressed genes described in OMIM.
Submitted: Dec 03, 2000
ORNL  
View Genome Sequence and Annotation View Different Annotated Features by Chromosome Gene Model Examples Annotate and Analyze New Genome Sequences.
Submitted: Sep 04, 2000
Primer3  
A form for making PCR selections. This tool offers a huge amount of parameters.
Submitted: Sep 04, 2000
Proteome & Genome Fasta33  
Search completed genomes and proteomes.
Submitted: Oct 24, 2000
Rat Genome Database  
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
RATMAP  
The Rat Genome Database: includes Searches, Maps, Homology, Nomenclature and more.
Submitted: Nov 19, 2000
READSEQ  
Converts input DNA/AA sequence to specified format (Input format is determined automatically).
Submitted: Nov 19, 2000
TIGR C. elegans Gene Index  
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
TIGR Drosophila Gene Index  
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
TIGR MOUSE Gene Index  
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
TIGR Rat Gene Index  
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
TMHMM  
Prediction of transmembrane helices in proteins.
Submitted: Dec 09, 2000
Transterm  
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
Web Signal Scan Service  
Find and list homologies of published signal sequences with the input DNA sequence.
Submitted: Nov 19, 2000
WebLogo  
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
Wise2  
Compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.
Submitted: Oct 15, 2000



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