Geneious
Encyclopedia
Geneious is suite of cross-platform bioinformatics
software applications developed by Biomatters Ltd.
, phylogenetics
and sequence analysis
. The Geneious Server will be capable of acting as a workstation or as a submit node to a Sun Grid Engine
Linux
cluster.
Biomatters are also currently in the private beta testing phase of the Geneious LIMS, a plugin that has been developed with the University of California Berkeley and the Smithsonian Institution
as part of the Moorea Biocode Project. The Geneious LIMS connects data in a field database to the data in the laboratory database and tracks the entire barcoding workflow from tissue sample, through DNA extraction
, PCR amplification, DNA sequencing reactions, 'barcode' contig assembly, binning, taxon verification and submission to BARSTOOL or BOLD databases at NCBI
. A generalized version of the Geneious LIMS plugin is expected to be provided as a free "Pro only" plugin to all researchers in the last quarter of 2010.
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
software applications developed by Biomatters Ltd.
Biomatters
Biomatters Limited is the company behind the Geneious Pro software, a bioinformatics software development company headquartered in Auckland, New Zealand. Biomatters develops sequence analysis and bioinformatics software capable of scaling from a single user to the enterprise level of...
Features
Geneious comes in a Basic version that is free for academic use, and a commercial Pro version with added features. Geneious bundles various bioinformatics tools under one hood with an easy-to-use email-client-like interface. See the release notes for a full list of features.- Fast de novo and reference assembly of illuminaIllumina (company)Illumina, Inc. is a company incorporated in April 1998 that develops, manufactures and markets integrated systems for the analysis of genetic variation and biological function. Using its technologies, the company provides a line of products and services that serve the sequencing, genotyping and...
, SOLiDApplied BiosystemsApplied Biosystems, Inc. started as GeneCo , was the name of a pioneer biotechnology company founded in 1981 in Foster City, California, in the San Francisco Bay Area...
, 454454 Life Sciences454 Life Sciences, is a biotechnology company based in Branford, Connecticut. It is a subsidiary of Roche, and specializes in high-throughput DNA sequencing.-History and Major Achievements:...
and Sanger data - Paired-end visualization
- Split viewer for genome browsing, easy restriction analysis and cloning workflows
- Virtual gel viewer
- Microsatellite viewer
- Sequence searching (NCBINCBINCBI may refer to:* National Center for Biotechnology Information, part of the U.S. National Institutes of Health* National Coalition Building Institute, a U.S. non-profit training group...
, PfamPfamPfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models.- Features :For each family in Pfam one can:* Look at multiple alignments* View protein domain architectures...
, UniprotUniProtUniProt is a comprehensive, high-quality and freely accessible database of protein sequence and functional information, many of which are derived from genome sequencing projects...
, BLASTBLASTIn bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
) and publication searching (PubMedPubMedPubMed is a free database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez information retrieval system...
, EntrezEntrezThe Entrez Global Query Cross-Database Search System is a powerful federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information website...
) - Automated search agents and smart agents - smart agents can be trained to search for other related documents
- Sequence alignmentSequence alignmentIn bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are...
and sequence viewing - BLASTBLASTIn bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
, MUSCLE, MAFFTMAFFTMAFFT is a multiple sequence alignment program for amino acid or nucleotide sequences. MAFFT is freely available for academic use, without any warranty.- External links :* * * at EBI* at GenomeNet* in MyHits, SIB...
, translation alignment, ClustalW on Greenbutton super-computer, MAUVE Genome Alignment - Motif search and open reading frameOpen reading frameIn molecular genetics, an open reading frame is a DNA sequence that does not contain a stop codon in a given reading frame.Normally, inserts which interrupt the reading frame of a subsequent region after the start codon cause frameshift mutation of the sequence and dislocate the sequences for stop...
prediction - Genome and protein annotations
- Phylogenetic treePhylogenetic treeA phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical and/or genetic characteristics...
building UPGMAUPGMAUPGMA is a simple agglomerative or hierarchical clustering method used in bioinformatics for the creation of phenetic trees...
, Neighbour joining with bootstrapping and consensus trees, PAUP*, MrBayes and PhyML plugin - Contig assembly and chromatogram editing
- in silico cloning and Gateway cloning - Restriction digest, insert and ligate into vector, add attB sites, PB reaction, LR reaction
- PCR Primer design - designing and testing, degenerate primers, mismatches and multiple primer searching, implementation of Primer3
- Protein structureProtein structureProteins are an important class of biological macromolecules present in all organisms. Proteins are polymers of amino acids. Classified by their physical size, proteins are nanoparticles . Each protein polymer – also known as a polypeptide – consists of a sequence formed from 20 possible L-α-amino...
viewer - Collaborate and share data over the internet
- Teach bioinformatics - Create tutorials with direct links to material in Geneious
- Public API to develop free bioinformaticsBioinformaticsBioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
plugin by the community - Sassafras K2 license server support
- Various standard bioinformatics applications such as ClustalClustalClustal is a widely used multiple sequence alignment computer program. The latest version is 2.1. There are two main variations:*ClustalW: command line interface*ClustalX: This version has a graphical user interface...
W, MrBayes, EMBOSSEMBOSSEMBOSS is an acronym for European Molecular Biology Open Software Suite. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology and bioinformatics user community...
, Mauve, MUSCLE and PAUP*
Future Directions
In news posted on their website, Biomatters plan to launch a new software product called Geneious Server in the second half of 2010 specifically to target the high intensity computational needs associated with Next Generation Sequence assemblyFull genome sequencing
Full genome sequencing , also known as whole genome sequencing , complete genome sequencing, or entire genome sequencing, is a laboratory process that determines the complete DNA sequence of an organism's genome at a single time...
, phylogenetics
Phylogenetics
In biology, phylogenetics is the study of evolutionary relatedness among groups of organisms , which is discovered through molecular sequencing data and morphological data matrices...
and sequence analysis
Sequence analysis
In bioinformatics, the term sequence analysis refers to the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution. Methodologies used include sequence alignment, searches against biological...
. The Geneious Server will be capable of acting as a workstation or as a submit node to a Sun Grid Engine
Sun Grid Engine
Oracle Grid Engine, previously known as Sun Grid Engine , previously known as CODINE or GRD , is an open source batch-queuing system, developed and supported by Sun Microsystems...
Linux
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...
cluster.
Biomatters are also currently in the private beta testing phase of the Geneious LIMS, a plugin that has been developed with the University of California Berkeley and the Smithsonian Institution
Smithsonian Institution
The Smithsonian Institution is an educational and research institute and associated museum complex, administered and funded by the government of the United States and by funds from its endowment, contributions, and profits from its retail operations, concessions, licensing activities, and magazines...
as part of the Moorea Biocode Project. The Geneious LIMS connects data in a field database to the data in the laboratory database and tracks the entire barcoding workflow from tissue sample, through DNA extraction
DNA extraction
DNA isolation is a routine procedure to collect DNA for subsequent molecular or forensic analysis. There are three basic and two optional steps in a DNA extraction:...
, PCR amplification, DNA sequencing reactions, 'barcode' contig assembly, binning, taxon verification and submission to BARSTOOL or BOLD databases at NCBI
National Center for Biotechnology Information
The National Center for Biotechnology Information is part of the United States National Library of Medicine , a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper...
. A generalized version of the Geneious LIMS plugin is expected to be provided as a free "Pro only" plugin to all researchers in the last quarter of 2010.
Other Software
- Gene Designer - A free gene design software suite with a range of design and cloning toolsGene DesignerGene Designer is a free bioinformatics software package. It is used by Molecular Biologists from academia, government and the pharmaceutical, chemical, agricultural and biotechnology industries to design, clone and validate genetic sequences.- Features :...
- ApE -A Multipurpose DNA Engineering Software, Donationware/Freeware
- Serial Cloner - A DNA editing and manipulating software for MacOS and Windows, Donationware/Freeware
- QuickGene - Mac OSX and Windows
- Gbench
- pDRAW32
- Discovery Studio
- Vector NTIVector NTIVector NTI is a bioinformatics software package. The current versions are v11.5.1 for Windows/PCs and v7.1 for Macs, but only supporting Mac OS X v10.3 .- Features :* create, annotate, analyse, and share DNA/protein sequences...
- CLC Main Workbench
- UGENEUGENEUGENE is free open-source cross-platform bioinformatics software.It integrates dozens of well-known biological tools and algorithms, providing both graphical user and command line interfaces...
- MacVectorMacVectorMacVector is a commercial sequence analysis application for Apple Macintosh computers running Mac OS X. It is intended to be used by Molecular Biologists to help analyze, design, research and document their experiments in the laboratory.- Features :...
External links
- Geneious Official website
- Biomatters website
- List of phylogeny software, hosted at the University of Washington