EMBOSS

EMBOSS is a free open source software analysis package developed for the needs of the molecular biology and bioinformatics user community.[1] 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.[2]

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.[3]

EMBOSS application groups

Group Description
AcdAcd file utilities
Alignment consensusMerging sequences to make a consensus
Alignment differencesFinding differences between sequences
Alignment dot plotsDot plot sequence comparisons
Alignment globalGlobal sequence alignment
Alignment localLocal sequence alignment
Alignment multipleMultiple sequence alignment
DisplayPublication-quality display
EditSequence editing
Enzyme kineticsEnzyme kinetics calculations
Feature tablesManipulation and display of sequence annotation
HMMHidden markov model analysis
InformationInformation and general help for users
MenusMenu interface(s)
Nucleic 2d structureNucleic acid secondary structure
Nucleic codon usageCodon usage analysis
Nucleic compositionComposition of nucleotide sequences
Nucleic CpG islandsCpG island detection and analysis
Nucleic gene findingPredictions of genes and other genomic features
Nucleic motifsNucleic acid motif searches
Nucleic mutationNucleic acid sequence mutation
Nucleic primersPrimer prediction
Nucleic profilesNucleic acid profile generation and searching
Nucleic repeatsNucleic acid repeat detection
Nucleic restrictionRestriction enzyme sites in nucleotide sequences
Nucleic RNA foldingRNA folding methods and analysis
Nucleic transcriptionTranscription factors, promoters and terminator prediction
Nucleic translationTranslation of nucleotide sequence to protein sequence
Phylogeny consensusPhylogenetic consensus methods
Phylogeny continuous charactersPhylogenetic continuous character methods
Phylogeny discrete charactersPhylogenetic discrete character methods
Phylogeny distance matrixPhylogenetic distance matrix methods
Phylogeny gene frequenciesPhylogenetic gene frequency methods
Phylogeny molecular sequencePhylogenetic molecular sequence methods
Phylogeny tree drawingPhylogenetic tree drawing methods
Protein 2d structureProtein secondary structure
Protein 3d structureProtein tertiary structure
Protein compositionComposition of protein sequences
Protein motifsProtein motif searches
Protein mutationProtein sequence mutation
Protein profilesProtein profile generation and searching
TestTesting tools, not for general use
Utils database creationDatabase installation
Utils database indexingDatabase indexing
Utils miscUtility tools

See also

References

  1. ↑ Rice P, Longden I, Bleasby A (2000). "EMBOSS: The European Molecular Biology Open Software Suite". Trends in Genetics. 16 (6): 276–277. doi:10.1016/S0168-9525(00)02024-2. PMID 10827456.
  2. ↑ Rice P, Bleasby A (1999). "EMBOSS: The European Molecular Biology Open Software Suite". Biochemist e-volution.
  3. ↑ http://emboss.open-bio.org/html/dev/ch01s01.html
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