The genetic content of a single set of chromosomes, or a single set of bacterial or viral genes.
View : Dr Chromo's school on the 'Genes'.
This is a search for genome in our database
- 1000 Fungal Genomes Project: Efforts to sequence 1000+ fungal genomes.
- A Gene Map of the Human Genome: The Human Genome Project is expected to produce a sequence of DNA representing the
functional blueprint and evolutionary history of the human species. However, only about 3% of
this sequence is thought to specify the portions of our 50,000 to 100,000 genes that encode
- A New Gene Map of the Human Genome: This new gene map represents such an index as
it includes the locations, within this text, of more
than 30,000 genes and provides an early
glimpse of some of the most important pieces of
the genome. Even more importantly, the map can
be immediately applied by scientists to the
identification and isolation of genes that either
directly cause human ailments or increase our
susceptibility to disease.
- Align against Greengenes (16S): Use this tool for aligning your set of 16S rRNA gene sequences using NAST or for finding near-neighbors or both. Each query sequence in your uploaded file will be searched for 16S rRNA gene sequences and aligned according to a Core Set of alignment templates. You can even upload a whole fasta genome and NAST will find, extract, and align the 16S rRNA genes for you. Additionally, Simrank (an N-mer comparison tool) will be used to find nearest-neighbors (non-chimeric) as well as nearest-isolates for each of your sequences from the entire Greengenes database...
- Artemis Home Page: Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation. Artemis is written in Java, and is available for UNIX, GNU/Linux, BSD, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK database entries or sequence in FASTA or raw format. Extra sequence features can be in EMBL, GENBANK or GFF format
- BEDTools: A powerful toolset for genome arithmetic.
- Berkeley Drosophila Genome Project: This new database represents one of the initial steps towards the ultimate construction of an
integrated Genome Projects- FlyBase database. Our current database contains data from the
Berkeley Drosophila Genome Project, the European Drosophila Genome Project, and genes and
aberrations that FlyBase has curated from the literature. In combination with the links to the
existing FlyBase database it represents a comprehensive collection that covers data from
laboratory to literature.
- BioToolKit (The): The restructured and updated BioToolKit, [***] an annotated directory of over 900 links to online molecular biology and neuroinformatics resources, includes basic research tools as well as advanced tools enabling integrated, multi-level analysis of the genome, transcriptome, and proteome.
- BIRCH - ACeDB: ACeDB is a database program that is both object-oriented and relational. Originally written for the C. elegans genome project, ACeDB has been used for virtually all plant and animal genome databases,
- Blat: Blat is an alignment tool like BLAST, but it is structured differently. On DNA, Blat works by keeping an index of an entire genome in memory. Thus, the target database of BLAT is not a set of GenBank sequences, but instead an index derived from the assembly of the entire genome.
- BROAD institute list of Software: Scientists in the Broad community have developed many critical software tools for the analysis of increasingly large genome-related datasets, and they make these tools openly available to the scientific community.
Chemical Biology, Image Analysis, Proteomics, Tool Suite, Visualization ,
Genetic Analysis, Genetic Variation, Linkage Analysis, Gene Expression,
Sequence Analysis, Assembly , Annotation, Alignment, RNAi, RNA-seq, Primer Design, Next Generation Tools , Phylogenetic Analysis, Gene Structure, Viral.
- BWA: Burrows-Wheeler Aligner: BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM.
- ChromDB: The Plant Chromatin Database: The mission of ChromDB is to bring together information on homologs of chromatin-associated proteins encoded by plant genomes, organize this information logically and in a comparative manner across species (with reference to other eukaryotes to the extent possible), and make it readily accessible to any members of the research and teaching communities who might be interested in the role played by chromatin proteins in the control of gene expression and genome organization. Our first priority is to provide (a) complete sets of genes encoding chromatin-associated proteins (CAPs) for those plant species with complete or near-complete genome sequences (currently Arabidopsis and rice, with poplar to be displayed in the future), (b) the best available splicing models and predicted protein sequences for these genes, and (c) a molecular phylogenetic context for understanding the evolutionary diversification of these protein families during plant evolution with reference to animal and fungal homologs. Our next priorities will be to identify and present CAP genes in all available EST and partial genomic sequences of other plant species, as well as to provide information regarding their biochemical, developmental, physiological, and cellular functions through a community annotation mechanism.
- Cocoa Genome Database: The release of the cacao genome sequence will provide researchers with access to the latest genomic tools, enabling more efficient research and accelerating the breeding process, thereby expediting the release of superior cacao cultivars.
- CoMet — a web-server for fast comparative functional profiling of metagenomes: CoMet allows you to compare the metabolic potential of metagenomes in terms of Pfam protein domains and the associated Gene Ontology (GO) terms. Our server implements a complete pipeline for functional profiling of multiple metagenomes: starting with an upload of multi-FASTA DNA sequence files (ideally one metagenome per file), subsequent ORF-finding is combined with a (very!) fast Pfam matching to compute the sequence assignments. Finally, a comparative statistical analysis based on pairwise tests on the assignment counts is performed to identify significantly differing domain families and GO-terms. The results include graphical and tabular output for a quick overview of the metagenomic differences.
- Computational Genomic Group (CGG): Computational approaches for analysis of nucleotide and protein sequences and structures as well as understanding structural and functional organization of genetic signals encoded in genome sequences.
- Courses and conferences at the Welcome Trust: Advanced Courses and Scientific Conferences are held in dedicated facilities at the Wellcome Trust Genome Campus in Hinxton, a short distance from the historic city of Cambridge.
- Euchromatin Network: Euchromatin is that portion of the genome that is most active in gene transcription within the animal cell nucleus. It is in marked contrast to heterochromatin, which is the least active. And yet, either form of chromatin can be converted to the other, conversion to euchromatin being associated with new gene activation for RNA synthesis, and conversion to heterochromatin being associated with new gene repression for RNA synthesis. // Together with the Euchromatin Network, we are developing forums on all aspects of euchromatin, its composition, activity, control, and significance. We welcome your comments and suggestions in the design of these forums, and your participation in their on-going discussions.
- Eukaryotic Genomes at JGI: From this site you can get details about our current and upcoming projects, or go directly to the individual genome sites.
All of the individual sites include direct access to download sequence files, BLAST, search, view and navigate the genomic annotations.
- Expressed Sequence Tags (dEST): dbEST (Nature Genetics 4:332-3;1993) is a division of GenBank that contains sequence data
and other information on "single-pass" cDNA sequences, or Expressed Sequence Tags, from a
number of organisms. A brief account of the history and current status of human ESTs in GenBank
is available (Trends Biochem. Sci. 20:295-6;1995). Also, consult the special "Genome Directory"
issue of Nature (vol. 377, issue 6547S, 28 September 1995).
- Genamics: With over 650 software entries, 360 journal speed links, and 100+ genome
project links, you can be assured that you can find what you need, and find
- GeneSpring Extras: Documentation;
External Programs and Databases;
Physical Position View;
- Genetic Education Center: For educators interested in human genetics and the human genome project.
- Genome Database: Established at Johns Hopkins University in Baltimore, Maryland, USA in 1990, the Genome
Database (GDB) is the official central repository for genomic mapping data resulting from the
Human Genome Initiative. The Human Genome Initiative is a worldwide research effort to analyze
the structure of human DNA and determine the location and sequence of the estimated 100,000
human genes. In support of this project, GDB stores and curates data generated worldwide by
those researchers engaged in the mapping effort of the Human Genome Project (HGP).
- Genome Jobs: Genome Jobs is the central resource for employment in Genomics, Bioinformatics, Biotechnology and
Biocomputing. We have listings of great career opportunities in Industry and Academia to save you time and
help sharpen your focus.
- HGMP-RC FUGU Project: The UK MRC HGMP-RC FUGU Project is a comparative mapping project funded by the MRC to allow Sydney Brenner and Greg Elgar,
through the HGMP, to generate a Landmark map of the puffer fish, Fugu rubripes (Fugu) genome.
- Human Genome Project: The Human Genome Project (HGP) was one of the great feats of exploration in history - an inward voyage of discovery rather than an outward exploration of the planet or the cosmos; an international research effort to sequence and map all of the genes - together known as the genome - of members of our species, Homo sapiens. Completed in April 2003, the HGP gave us the ability to, for the first time, to read nature\'s complete genetic blueprint for building a human being.
- Human Genome Sequencing Center at Baylor College of Medicine: Large-scale genomic sequencing at Baylor College of Medicine began in 1993 in the laboratory of Dr. Richard Gibbs. The
Baylor College of Medicine Human Genome Sequencing Center was established in 1996 as a one of six large-scale sequencing
pilot projects funded by NHGRI.
- Integrated Genomics ERGO: ERGO Genome Analysis and Discovery System is an in silico systems biology platform for the comprehensive analysis of organisms. ERGO is developed by Integrated Genomics.
- JGI: Genome Portal: The Joint Genome Institute has released 110 Eukaryotic sites, 406 Prokaryotic microbial sites (with 281 complete).
From this site you can get details about our current and upcoming projects. We also
- Karyn\'s Genomes: This is a collection and brief description of some of the available sequenced genomes. There is also information about why they are thought to be important for sequencing, together with links to the sequences, publication data and further reading.
- KEGG: Kyoto Encyclopedia of Genes and Genomes: A grand challenge in the post-genomic era is a complete computer representation of the cell, the organism, and the biosphere, which will enable computational prediction of higher-level complexity of cellular processes and organism behaviors from genomic and molecular information. Towards this end we have been developing a bioinformatics resource named KEGG as part of the research projects of the Kanehisa Laboratories in the Bioinformatics Center of Kyoto University and the Human Genome Center of the University of Tokyo.
- Littel book of R: This is a simple introduction to bioinformatics, with a focus on genome analysis, using the R statistics software.
- Mapping and Sequencing the Human Genome: A primary goal of the Human Genome Project is to make a series of descriptive diagrams mapsof
each human chromosome at increasingly finer resolutions.
- Mauve Genome Alignment Software : Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.
- MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks: MetaNetX.org is a website for accessing, analysing and manipulating genome-scale metabolic networks (GSMs) as well as biochemical pathways. It consistently integrates data from various public resources and makes the data accessible in a standardized format using a common namespace. Currently, it provides access to hundreds of GSMs and pathways that can be interactively compared (two or more), analysed (e.g. detection of dead-end metabolites and reactions, flux balance analysis or simulation of reaction and gene knockouts), manipulated and exported. Users can also upload their own metabolic models, choose to automatically map them into the common namespace and subsequently make use of the website’s functionality.
- Metnet:: plant pathways Database: MetNet is in-development, publicly available software for analysis of genome-wide mRNA, protein, and metabolite profiling data. The software is designed to enable the biologist to visualize, statistically analyze, and model a metabolic and regulatory network map of Arabidopsis, combined with gene expression profiling data.
MetNet will provide a framework for the formulation of testable hypotheses regarding the function of specific genes, and in the long term will provide the basis for identification of metabolic and regulatory networks that control plant composition and development.
- Micorbial Genomes at JGI (USA): From this site you can get details about our current and upcoming projects, or go directly to the individual microbial genome sites. All of the individual sites include direct access to download sequence file(s), BLAST, and view annotations. Additionally, the Eukaryotic microbial sites include more advanced visualization and search tools.
- MIRA Assembler: MIRA - Sequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data. Can use Sanger, 454, Illumina and IonTorrent data. PacBio: CCS and error corrected data usable, uncorrected not yet.
- NASC: nottingham Arabidopsis Stock Center: The Nottingham Arabidopsis Stock
Centre (NASC) provides seed and
information resources to the
International Arabidopsis Genome
Programme and the wider research
- NCBI Genome Workbench: NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data.
- NCBI: National Center for Biotechnology Information: Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease.
- OmniMapFree: OmniMapFree is a computer program for displaying and analysing the genome of any organism. You can use it to generate genome maps of your own favourite organism and to link chromosome, genetic, transcriptomic, proteomic, molecular mutant and many other types of important information directly to the genomic sequence. It is very easy to use - it does not require any knowledge of databases or computer programming. All of the data is held in plain text files which can be created and modified using a simple text editor e.g. Notepad or Wordpad.
- Primer on Molecular Genetics (Department of energy): This primer was prepared by Denise Casey (Human Genome Management Information System - Oak Ridge
National Laboratory) for the 1991-92 DOE Human Genome Program Report and modified for Web access by
- Principe des DNA sur Puce: Les puces à ADN permettent de mesurer et de visualiser très rapidement les différences d'expression entre les gènes et ceci à l'échelle d'un
génome complet. Si la mise en oeuvre de la technique est assez compliquée, son principe est très simple. En voici les principales étapes
- SNAP: SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser.
- Softberry: Huge collection of software for the analysis and annotation of sequences and genomes.
- STRING: Search Tool for Recurring Instances of Neighbouring Genes: STRING is a comparative genome analyis tool that detects whether a given query gene occurs repeatedly with certain other genes in potential
- The Draft Human Genome Sequence, an Introduction: Anyone with a computer and an Internet connnection can now explore the draft sequence of the human genome. How can molecular biologists capitalize on these data riches, and what are the advantages of using the assembled draft sequence? This website aims to jump-start those who want make use of this information, but are not sure where or how to start.
- The Ensembl Project: Ensembl is a joint project between EMBL-EBI and the Sanger Centre to
develop a software system which produces and maintains automatic
annotation on eukaryotic genomes.
- The GDB Browser: The Genome Database (GDB) stores and curates genomic mapping data submitted by researchers
worldwide and provides this information electronically to the scientific community. Getting Started
- TIGR - Comprehensive Microbial Resource: The Comprehensive Microbial Resource (CMR) is a free website used to display information on all of the publicly available, complete prokaryotic genomes. In addition to the convenience of having all of the organisms on a single website, common data types across all genomes in the CMR make searches more meaningful, and cross genome analysis highlight differences and similarities between the genomes.
- TIGR - Genome Projects: TIGR\'s Genome Projects are a collection of curated databases containing DNA and protein sequence, gene expression, cellular role, protein family, and taxonomic data for microbes, plants and humans.
- Tutorial on Artemis: The purpose of this tutorial is to introduce new users to some of the tools in Artemis that are most relevant to analyses of the P .syringae genomes.
- UGENE - Unipro: UGENE is a free cross-platform genome analysis suite.
Multiple sequence alignment using MUSCLE 3,4 and KAlign;
HMM profiles build and search, based on the source of HMMER 2 and HMMER 3;
PCR Primers design using Primer 3;
Protein secondary structure prediction using GOR IV and PSIPRED;
Phylogenetic analysis with Phylip;
Search for restriction enzymes and integration with REBASE;
Extremely fast repeat finder;
DNA reference assembly using Bowtie;
Search for transcription factor binding sites using SITECON;
Protein back translation;
Complete Smith-Waterman algorithm implementation;
Comparing genomes using dotplot view.
- vcftools: A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project