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| ACMES - http://acmes.rnet.missouri.edu/ ACMES (Advanced Content Matching Engine for Sequences) is a server that can be used to search for short repeats (between 3 and 10 000 bases) across multiple species. Users can limit results of a search by keyword searches. - [Read more ACMES] |
| AlignACE - http://arep.med.harvard.edu/mrnadata/mrnasoft.html Aligns Nucleic Acid Conserved Elements; uses pattern recognition to find elements conserved in a set of DNA sequences; free for non-commercial use with license agreement. - [Read more AlignACE] |
| BEARR - http://giscompute.gis.a-star.edu.sg/~vega/BEARR1.0/ Batch Extraction and Analysis of cis-Regulatory Regions (BEARR) takes a list of gene identifiers (such as RefSeq and Unigene IDs), consensus patterns, and (optionally) a position weight matrix as input and returns a list of matches for the patterns in bot - [Read more BEARR] |
| BioMart - http://www.ebi.ac.uk/biomart/ BioMart is an interactive data integration system facilitating large-scale data queries. It can be installed and used in-house, or with one of the existing data sources to which is has already been applied (ie. UniProt, Ensembl). - [Read more BioMart] |
| BioProspector - http://robotics.stanford.edu/~xsliu/BioProspector/ Server which scans upstream of genes in the same gene expression cluster for regulatory sequence motifs using a Gibbs sampling strategy. The Markov background model is used for non-motif bases, improving specificity of predicted motif locations. - [Read more BioProspector] |
| Codon Usage Database - http://www.kazusa.or.jp/codon/ Find GC content and frequency of codon usage for any organism that has a sequence in GenBank. - [Read more Codon Usage Database] |
| CompareProspector - http://compareprospector.stanford.edu/ Server which attempts to identify any motifs related to genes predicted to share regulatory elements. It alters Gibbs sampling through biasing searches towards conserved sequences across multiple species. - [Read more CompareProspector] |
| Consite - http://www.phylofoot.org/consite/ Detect transcription factor binding sites in genomic sequences using phylogenetic footprinting and experimentally-confirmed binding profiles. - [Read more Consite] |
| CREME - http://creme.dcode.org/ CREME (Cis-Regulatory Module Explorer for the human genome) is a tool for identifying and visualizing cis-regulatory modules for a given set of genes that are potentially co-expressed or co-regulated. It takes as input a list of accession numbers, and re - [Read more CREME] |
| Drosophila DNase I footprint database - http://www.flyreg.org/ Database of transcription factor binding sites created from systematic literature curation and genome annotation of DNase I footprints for Drosophila. - [Read more Drosophila DNase I footprint database] |
| eBioinformatics - http://www.ebioinformatics.org/ This site provides several bioinformatics software tools packaged together for easy installation on MacOSX computers. The software includes NCBI tools, EMBOSS, ClustalW, Staden, T-Coffee and Primer3. - [Read more eBioinformatics] |
| EMBOSS - http://cbrmain.cbr.nrc.ca/EMBOSS/ Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. - [Read more EMBOSS] |
| Eponine - http://www.sanger.ac.uk/Users/td2/eponine/ Eponine is a probabilistic method for detecting transcription start sites (TSS) in mammalian genomic sequence, with good specificity and excellent positional accuracy. - [Read more Eponine] |
| FAN - http://bioinf.man.ac.uk/cgi-bin/neil/ntfront.pl FAN (Fingerprint Analysis of Nucleotide sequences) searches nucleotide sequences against the PRINTS database, a collection of protein fingerprints used to assign uncharacterised sequences to known families and hence to infer tentative functions. - [Read more FAN] |
| FirstEF - http://rulai.cshl.org/tools/FirstEF/ First Exon Finder (FirstEF) is a 5' terminal exon and promoter prediction program. It consists of different discriminant functions structured as a decision tree. - [Read more FirstEF] |
| GCUA: Graphical Codon Usage Analyser - http://gcua.schoedl.de Graphical representation of codon bias - [Read more GCUA: Graphical Codon Usage Analyser] |
| Gibbs Motif Sampler - http://bayesweb.wadsworth.org/gibbs/gibbs.html This tool allows you to identify motifs or conserved regions in protein or DNA sequences. - [Read more Gibbs Motif Sampler] |
| Harvester - http://harvester.embl.de/ Harvester provides fast access to public bioinformatic databases and servers for human proteins. Results are returned as a single HTML page that contains the cached and cross-linked output from the following databases/servers: Uniprot/SWISSprot, ensEMBL, - [Read more Harvester] |
| IBM Bioinformatics and Pattern Discovery Group - http://cbcsrv.watson.ibm.com/Tspd.html Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detail - [Read more IBM Bioinformatics and Pattern Discovery Group] |
| IslandPath - http://www.pathogenomics.sfu.ca/islandpath/ IslandPath aids genomic island detection in prokaryotic genome seqeunces, using features such as dinucleotide bias, G+C, location of tRNA genes, annotations of mobility genes, etc. Genomic islands are defined here as genomic regions of potential horizonta - [Read more IslandPath] |
| IsoFinder - http://bioinfo2.ugr.es/IsoF/isofinder.html IsoFinder is a tool for the prediction of isochores for a user-supplied sequence. - [Read more IsoFinder] |
| JASPAR - http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl JASPAR is a non-redundant, curated collection of transcription factor binding profiles. Each profile is generated from published, experimentally defined eukaryotic transcription factor binding sites. - [Read more JASPAR] |
| LowComplexity - http://wwwmgs.bionet.nsc.ru/mgs/programs/low_complexity/ LowComplexity is a tool that searches for low complexity regions of DNA or protein sequences. Using LowComplexity you can search long sequences (chromosomes, genomes) or a set of aligned sequences. This resource also contains links to other algorithms f - [Read more LowComplexity] |
| MartView - http://www.ensembl.org/Multi/martview The Ensembl EnsMart Genome Browser (MartView) is a tool for data retrieval and data mining that integrates data from Ensembl. Through the web interface MartView allows you to apply a series of filters to create custom datasets which can be converted to s - [Read more MartView] |
| MaskerAid - http://blast.wustl.edu/maskeraid/ MaskerAid is an enhancement to RepeatMasker which can effect about a 30-fold increase in the speed of RepeatMasker while maintaining sensitivity. - [Read more MaskerAid] |
| MatInspector - http://www.gene-regulation.com/pub/programs.html#matinspector Search for potential transcription factor binding sites in your own sequences using TRANSFAC matrices; free for non-commercial use. - [Read more MatInspector] |
| McPromoter - http://genes.mit.edu/McPromoter.html The Markov Chain Promoter Prediction Server (McPromoter) uses statistics to predict eukaryotic DNA transcription start sites. - [Read more McPromoter] |
| MDscan - http://robotics.stanford.edu/~xsliu/MDscan/ Server designed to pinpoint protein-DNA interaction sites at the base pair level. Uses ChIP-array data, word enumeration and position-specific weight matrix updating to search for motifs representing these interaction sites. - [Read more MDscan] |
| MEME - http://meme.sdsc.edu/meme/website/meme.html Analyzes a set of DNA or protein sequences for similarities among them and produces a description (motif) for each pattern it discovers. - [Read more MEME] |
| Meta-MEME - http://metameme.sdsc.edu/ Creates hidden Markov model of motif from MEME output and searches sequence database for matches to this motif. - [Read more Meta-MEME] |
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