EMBOSS is a free c software analysis package developed for the needs of the molecular biology and bioinformatics user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole.
EMBOSS is an acronym for European Molecular Biology Open Software Suite. The European part of the name hints at the wider scope. The core EMBOSS groups are collaborating with many other groups to develop the new applications that the users need. This was done from the beginning with EMBnet, the European Molecular Biology Network. EMBnet has many nodes worldwide most of which are national bioinformatics services. EMBnet has the programming expertise. In September 1998, the first workshop was held, when 30 people from EMBnet went to Hinxton to learn about EMBOSS and to discuss the way forward.
The EMBOSS package contains a variety of applications for sequence alignment, rapid database searching with sequence patterns, protein motif identification (including domain analysis), and much more.
The AJAX and NUCLEUS libraries are released under the GNU Library General Public Licence. EMBOSS applications are released under the GNU General Public Licence.
EMBOSS application groups GroupDescriptionAcd Acd file utilitiesAlignment consensus Merging sequences to make a consensusAlignment differences Finding differences between sequencesAlignment dot plots Dot plot sequence comparisonsAlignment global Global sequence alignmentAlignment local Local sequence alignmentAlignment multiple Multiple sequence alignmentDisplay Publication-quality displayEdit Sequence editingEnzyme kinetics Enzyme kinetics calculationsFeature tables Manipulation and display of sequence annotationHMM Hidden markov model analysisInformation Information and general help for usersMenus Menu interface(s)Nucleic 2d structure Nucleic acid secondary structureNucleic codon usage Codon usage analysisNucleic composition Composition of nucleotide sequencesNucleic CpG islands CpG island detection and analysisNucleic gene finding Predictions of genes and other genomic featuresNucleic motifs Nucleic acid motif searchesNucleic mutation Nucleic acid sequence mutationNucleic primers Primer predictionNucleic profiles Nucleic acid profile generation and searchingNucleic repeats Nucleic acid repeat detectionNucleic restriction Restriction enzyme sites in nucleotide sequencesNucleic RNA folding RNA folding methods and analysisNucleic transcription Transcription factors, promoters and terminator predictionNucleic translation Translation of nucleotide sequence to protein sequencePhylogeny consensus Phylogenetic consensus methodsPhylogeny continuous characters Phylogenetic continuous character methodsPhylogeny discrete characters Phylogenetic discrete character methodsPhylogeny distance matrix Phylogenetic distance matrix methodsPhylogeny gene frequencies Phylogenetic gene frequency methodsPhylogeny molecular sequence Phylogenetic molecular sequence methodsPhylogeny tree drawing Phylogenetic tree drawing methodsProtein 2d structure Protein secondary structureProtein 3d structure Protein tertiary structureProtein composition Composition of protein sequencesProtein motifs Protein motif searchesProtein mutation Protein sequence mutationProtein profiles Protein profile generation and searchingTest Testing tools, not for general useUtils database creation Database installationUtils database indexing Database indexingUtils misc Utility tools
See also Open Bioinformatics Foundation Soaplab - A SOAP web service interface including EMBOSS Genostar - Integration of some of EMBOSS tools in a graphical application
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