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AMIGene -- Annotation of MIcrobial Genes
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| Automatically identify the most likely coding sequences (CDSs) in a large contig or a complete bacterial genome sequence.
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BABELOMICS -- advanced functional profiling of transcriptomics, proteomics and genomics experiments
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| Suite of web tools for the functional profiling of genome scale experiments.
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BASys -- a web server for automated bacterial genome annotation
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| Perform automated and in-depth annotation of bacterial genomes.
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BRIGEP — the BRIDGE-based genome–transcriptome–proteome browser
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| Process and analyze bacterial genome, transcriptome and proteome data.
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Bioverse -- functional, structural and contextual annotation of proteins and proteomes
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| Perform protein and proteome annotations.
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CAPweb -- a bioinformatics CGH array Analysis Platform
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| Analyze, visualize and interpret comparative genomic hybridization (CGH) data.
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CNVDetector -- locating copy number variations using array CGH data
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| A program for locating copy number variations in a single genome.
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CREx -- Common interval Rearrangement Explorer
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| Infer genomic rearrangements based on common intervals.
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CanGEM -- Cancer GEnome Mine
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| A public database for storing clinical information about tumor samples and microarray data, emphasizing array comparative genomic hybridization (aCGH) and data mining of gene copy number changes.
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DNannotator -- annotation software tool kit for regional genomic sequences
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| Perform batch annotation on a sizable genomic region.
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Dcode.org anthology of comparative genomic tools
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| Demarcate functional regions in genomic DNA sequences using a list of tools.
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ECR Browser -- A Tool for Visualizing and Accessing Data from Comparisons of Multiple Vertebrate Genomes
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| Access to whole genome alignments of human, mouse, rat and fish sequences. |
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ESTAnnotator -- a tool for high throughput EST annotation
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| Perform high throughput annotation of expressed sequence tags (ESTs). |
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Ensembl
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| Find genome annotation, databases and other information for chordate and selected model organism and disease vector genomes. |
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EnteriX 2003 -- Visualization tools for genome alignments of Enterobacteriaceae
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| Use a suite of three web-based visualization tools to graphically display alignment information from comparisons among several fixed and user-supplied sequences from related enterobacterial species, anchored on a reference genome.
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GC-Profile -- a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences
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| Analyze the variation of GC content in genomic sequences.
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GEAR -- genomic enrichment analysis of regional DNA copy number changes
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| Interpret genome-wide DNA copy number changes identified by array-based comparative genomic hybridization.
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GENESIS -- genome evolution scenarios
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| Solve genome rearrangement problems.
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Iccare -- Merge Sequence and Mapping Information for Plant and Animal Species
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| Annotate crude EST (expressed sequence tag) specifically dedicated to comparative mapping approaches. |
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Identification of patterns in biological sequences at the ALGGEN server -- PROMO and MALGEN
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| Predict of transcription factor binding sites or visualize sequence correspondences among long DNA sequences. |
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IsoFinder -- Computational Prediction of Isochores in Genome Sequences
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| Predict isochores at the genomic sequence level.
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KAAS -- KEGG Automatic Annotation Server
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| Provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database.
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MADAP -- a flexible clustering tool for the interpretation of one-dimensional genome annotation data mapped onto complete or partial genome sequences.
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| Interpret genome annotation data mapped onto complete or partial genome sequences.
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MAVID multiple alignment server
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| Quickly obtain multiple alignments for genomic sequences and to subsequently Analise the alignments for conserved regions.
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MGAlignIt -- a web service for the alignment of mRNA/EST and genomic sequences
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| Align mRNA or expressed sequence tags (EST) and genome sequences.
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MICheck -- a web tool for fast checking of syntactic annotations of bacterial genomes
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| Perform rapid verification of sets of annotated genes and frameshifts in previously published bacterial genomes.
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Manipulating multiple sequence alignments via MaM and WebMaM
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| Process and manipulate multiple alignments of genomic sequence.
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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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Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC
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| Perform multiple alignment of genomic sequences.
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PLOTREP -- a web tool for defragmentation and visual analysis of dispersed genomic repeats
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| Identify interspersed repetitive elements in BAC-sized or smaller genomic regions.
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Phydbac2 -- Phylogenomic Display of Bacterial Genes
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| Display phylogenomic profiles of bacterial protein sequences and infer pairwise gene functional relationships.
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Proteomes and Genomes Fasta
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| Perform sequence similarity searching against complete genomes databases using the Fasta programs.
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SPRING -- a tool for the analysis of genome rearrangement using reversals and block-interchanges
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| Analyze genome rearrangement between two chromosomal genomes.
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The CHAOS/DIALIGN -- Multiple Alignment of Genomic Sequences
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| Perform multiple alignment of large genomic sequences.
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The UCSC Archaeal Genome Browser
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| Browse archaeal genomes. |
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UCSC Genome Browser
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| Get a rapid and reliable display of any requested portion of genomes at any scale, together with dozens of aligned annotation tracks. |
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WILMA -- A genome and proteome annotation system
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| Search for genomes of nematode C.elegans, Homo sapiens, Mus musculus, Arabidopsis thaliana, all annotated by WILMA annotation system. |
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WebGestalt -- an integrated system for exploring gene sets in various biological contexts
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| Search and analyze comprehensive genetic information of a set of genes. |
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X:Map -- annotation and visualization of genome structure for Affymetrix exon array analysis
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| A project for mapping between Affymetrix Exon Arrays and their corresponding genome data.
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ZOOM! -- Zillions Of Oligos Mapped
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| Designed to map millions of short reads, emerged by next-generation sequencing technology, back to the reference genomes, and carry out post-analysis.
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e2g -- An Interactive Web-based Server for Efficiently Mapping Large EST and cDNA Sets to Genomic Sequences
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| Map large expressed sequence tag (EST) and cDNA datasets to genomic DNA.
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g:Profiler -- a web-based toolset for functional profiling of gene lists from large-scale experiments
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| A public web server for characterising and manipulating gene lists resulting from mining high-throughput genomic data.
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