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A comprehensive BAC resource
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| Search this comprehensive BAC resource to find the available mapping, sequence, annotation and functional data for each BAC for different species.
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ACLAME -- A CLAssification of Mobile genetic Elements
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| Search and classify prokaryotic mobile genetic elements (MGEs).
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AGenDA -- Gene Prediction by Cross-species Sequence Comparison
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| Predict genes by comparing genomic sequences from evolutionary related organisms to each other.
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AUGUSTUS -- ab initio prediction of alternative transcripts
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| Predict gene in eukaryotic genomic sequences based on a generalized hidden Markov model.
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AlterORF -- a database of alternate open reading frames
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| A searchable databse of alternate ORFs for over 600 fully sequenced microbial genomes.
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BAGEL -- a web-based bacteriocin genome mining tool
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| Predict putative bacteriocin open reading frames (ORFs) in a DNA sequence.
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BLogo -- A tool for visualization of bias in biological sequences
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| Detects and displays statistically significant position-specific sequence bias with reduced background noise.
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Blast2 EVEC
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| Find vector contamination in a nucleotide sequences.
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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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CSTminer -- A web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison
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| Identify coding and noncoding conserved sequence tags through cross-species genome comparison.
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CUTG -- Codon usage tabulated from the international DNA sequence databases
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| Find the sum of the codon use of an organism from a list of 23093 organisms (2004).
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ChimerDB -- A Knowledgebase for fusion sequences
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| Search for fusion sequences in human, mouse and rat genomes.
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CodonO -- codon usage bias analysis within and across genomes
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| Measure synonymous codon usage bias within and across genomes.
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Complexity -- An Internet resource for analysis of DNA sequence complexity
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| Search for low complexity regions in long sequences and estimate complexity of groups of aligned sequences.
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CpGPlot/CpGReport/Isochore
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| Find CpG island in a nucleotide sequence.
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DiProDb -- Dinucleotide Property Database
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| Find information about dinucleotide molecular properties.
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EUGÈNE'HOM -- a generic similarity-based gene finder using multiple homologous sequences
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| Predict eukaryotic genes based on comparative analysis of homologous sequences.
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EasyGene -- a prokaryotic gene finder that ranks ORFs by statistical significance.
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| Predict and statistically evaluate predicted prokaryotic open reading frames (ORFs).
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Entrez Gene -- gene-centered information at NCBI
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| Search for gene-specific information in NCBI database.
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FeatureExtract — extraction of sequence annotation made easy
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| Extract sequence and feature annotation, such as intron/exon structure, from GenBank entries and other GenBank format files.
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FrameD -- a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences
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| Predict coding regions in prokaryotic and matured eukaryotic sequences.
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GASCO -- genetic algorithm simulation for codon optimization
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| An algorithm developed for the optimum codon selection using genetic algorithms.
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GENSTYLE -- exploration and analysis of DNA sequences with genomic signature
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| Characterize and classify nucleotide sequences based on the genomic signature paradigm.
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GenScan --Finding the genes in genomic DNA
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| To predict the locations and exon-intron structures of genes in genomic sequences from vertebrate,invertebrate and plants.
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GeneAlign -- a coding exon prediction tool based on phylogenetical comparisons
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| Predict coding sequences.
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GeneFizz -- a web tool to compare genetic (coding/non-coding) and physical (helix/coil) segmentations of DNA sequences. Gene discovery and evolutionary perspectives
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| Compare between genetic (coding/non-coding) and physics (helix/coil) segmentations of DNA sequences.
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GeneMark -- web software for gene finding in prokaryotes, eukaryotes and viruses
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| Predict genes in prokaryotic, eukaryotic and viral genomic sequences.
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GlimmerM, Exonomy and Unveil -- three ab initio eukaryotic genefinders
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| Predict genes in DNA sequences with different software tools.
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HERVd -- Human Endogenous Retrovirus Database
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| Screen human genome for Human endogenous retroviruses (HERVs).
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HOPPSIGEN -- A database of human and mouse processed pseudogenes
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| Search for information on annotate processed pseudogenes in complete genomes.
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HUMHOT -- a database of human meiotic recombination hot spots
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| Search for meiotic recombination spots in human genome.
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ISfinder -- the reference centre for bacterial insertion sequences
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| Search for bacterial insertion sequences (ISs).
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Integrated databanks access and sequence/structure analysis services at the PBIL
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| Access to sequence databanks and to many tools of nucleic acid and protein sequence analyses. |
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Islander -- integrative islands in prokaryotic genome
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| To search for islands in prokarytoic genomic DNA sequences and analyze the phylogeny of the associated integrases.
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JCat -- a novel tool to adapt codon usage of a target gene to its potential expression host
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| Adapt target gene codon usage to expression hosts to improve heterologous protein synthesis.
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LTR_FINDER -- an efficient tool for the prediction of full-length LTR retrotransposons
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| Find full-length LTR retrotransposons in genome sequences.
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MICdb -- A database of prokaryotic microsatellites
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| Search for non-redundant microsatellites extracted from fully sequenced prokaryotic genomes.
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MKT -- The McDonald and Kreitman test
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| Detect the signature of natural selection at the molecular level.
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MicroRNA.org -- targets and expression resource
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| Find microRNA target predictions and expression profiles in this comprehensive resource. |
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NCBI ORF Finder
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| Find open reading frames(ORF) present in a nucleotide sequence.
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NPRD -- Nucleosome Positioning Region Database
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| Search for experimental data on locations and characteristics of nucleosome formation sites.
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OPTIMIZER -- a web server for optimizing the codon usage of DNA sequences
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| An on-line PHP application that optimizes the codon usage of a DNA sequence to increase its expression level.
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ORFDB --A High-quality Open Reading Frame Collection
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| Search an evolving collection of human and mouse Open Reading Frame (ORF) clones (UltimateTM ORF Clones). |
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OrfPredictor -- predicting protein-coding regions in EST-derived sequences
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| Identify protein-coding regions in expressed sequence tag (EST)-derived sequences.
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OrthoMCL-DB -- querying a comprehensive multi-species collection of ortholog groups
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| Search for predicted ortholog group from 55 species. |
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ProMiR II -- a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs
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| Predict miRNA genes. |
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RBR -- library-less repeat detection for ESTs
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| Mask ESTs for repeats, without using a library.
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RTAnalyzer -- a web application for finding new retrotransposons and detecting L1 retrotransposition signatures
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| Tracks sequences of retrotransposed origin by scoring the signature results from an L1-mediated insertion within a genome.
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RefSeq -- Reference Sequence database
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| Find sequences representing genomes, transcripts, and proteins. |
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SGDB -- a database of synthetic genes re-designed for optimizing protein over-expression
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| Search for sequences and associated experimental information on synthetic (artificially engineered) genes from all peer-reviewed studies.
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STRBase -- A short tandem repeat DNA database for the human identity testing community
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| Search for short tandem repeat DNA in human genome.
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Sircah -- a tool for the detection and visualization of alternative transcripts
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| Detect, analyze and visualize alternative transcripts.
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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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TACT -- Transcriptome Auto-annotation Conducting Tool of H-InvDB
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| Conduct functional annotation of mRNA transcripts.
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TargetIdentifier -- a web server for identifying full-length cDNAs from EST sequences
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| Identify full-length EST cDNAs and functionally annotate EST cDNAs.
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The Genetic Codes at NCBI
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| Search for comprehensive information on genetic codes.
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The Gypsy Database (GyDB) of mobile genetic elements
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| An in-progress database devoted to the non-redundant analysis and evolutionary-based classification of mobile genetic elements.
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The TIGR Gene Indices -- clustering and assembling EST and known genes and integration with eukaryotic genomes
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| Search for annotated genetic information of expressed sequence tags (ESTs) in different eukaryotic organisms.
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The imprinted gene and parent-of-origin effect database
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| Search for information on animal genes and phenotypes for which parent-of-origin effects have been reported.
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The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs
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| Search for tRNA genes and snoRNA genes in genomic sequences.
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The web server of IBM's Bioinformatics and Pattern Discovery group
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| Access to a large number of software tools for various bioinformatics tasks. |
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TranspoGene -- The influence of Transposed Elements (TEs) on the transcriptome of 7 species
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| Contains information regarding specific type and family of the TEs, genomic and mRNA location, sequence, supporting transcript accession and alignment to the TE consensus sequence.
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Transterm -- A database of mRNAs and translational control elements
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| Search for elements and biologically relevant regions in mRNAs that control translation.
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UCbase & miRfunc -- Ultraconserved sequences and miRNA function database
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| Search for information about ultraconserved regions, miRNAs and their related human disorders and genomic properties.
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UTR BLAST
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| Search for the presence of UTR elements in a nucleotide sequence.
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UTR Scan
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| Search for UTR functional elements in query sequences.
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UTRome.org -- a platform for 3'UTR biology in C. elegans
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| Find 3'UTRs and their functional elements in C. elegans, including 3'UTR sequences, graphical displays, predicted and validated functional elements, secondary structure predictions, and other detailed data.
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UgMicroSatdb -- database for mining microsatellites from unigenes
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| A web-based relational database of microsatellites present in unigene sequences covering 80 genomes.
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UniGene
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| Find mapping and expression information for a unigene cluster (ESTs and full-length mRNA sequences organized into clusters that each represent a unique known or putative gene)
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UniVec -- Identify DNA segments may be of vector origin
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| Identify vector contamination in nucleic acid sequences.
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VecScreen
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| Find vector sequence contamination in a nucleotide sequence
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VectorDB -- A database of commonly used vectors sequences
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| Search for annotations and sequence information for many vectors commonly used in molecular biology.
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Xpro -- A database of eukaryotic protein-encoding genes
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| Search all the eukaryotic protein-encoding DNA sequences contained in GenBank and find annotations on the splice sites and intron phases.
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miRBase -- tools for microRNA genomics
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| Search for comprehensive microRNA sequence data, annotation and predicted gene targets. |
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microTranspoGene -- The influence of Transposed Elements (TEs) on the biogenesis of microRNAs
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| Locate TE-derived microRNAs.
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piRNABank -- a web resource on classified and clustered Piwi-interacting RNAs
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| Provides information on piRNAs in Human, Mouse, Rat, and Drosophila.
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Éclair — a web service for unravelling species origin of sequences sampled from mixed host interfaces
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| Use support vector machines for the classification of the origin of expressed sequence tags stemming from mixed host cDNA libraries.
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