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 |
|---|---|
| Acd | Acd file utilities |
| Alignment consensus | Merging sequences to make a consensus |
| Alignment differences | Finding differences between sequences |
| Alignment dot plots | Dot plot sequence comparisons |
| Alignment global | Global sequence alignment |
| Alignment local | Local sequence alignment |
| Alignment multiple | Multiple sequence alignment |
| Display | Publication-quality display |
| Edit | Sequence editing |
| Enzyme kinetics | Enzyme kinetics calculations |
| Feature tables | Manipulation and display of sequence annotation |
| HMM | Hidden markov model analysis |
| Information | Information and general help for users |
| Menus | Menu interface(s) |
| Nucleic 2d structure | Nucleic acid secondary structure |
| Nucleic codon usage | Codon usage analysis |
| Nucleic composition | Composition of nucleotide sequences |
| Nucleic CpG islands | CpG island detection and analysis |
| Nucleic gene finding | Predictions of genes and other genomic features |
| Nucleic motifs | Nucleic acid motif searches |
| Nucleic mutation | Nucleic acid sequence mutation |
| Nucleic primers | Primer prediction |
| Nucleic profiles | Nucleic acid profile generation and searching |
| Nucleic repeats | Nucleic acid repeat detection |
| Nucleic restriction | Restriction enzyme sites in nucleotide sequences |
| Nucleic RNA folding | RNA folding methods and analysis |
| Nucleic transcription | Transcription factors, promoters and terminator prediction |
| Nucleic translation | Translation of nucleotide sequence to protein sequence |
| Phylogeny consensus | Phylogenetic consensus methods |
| Phylogeny continuous characters | Phylogenetic continuous character methods |
| Phylogeny discrete characters | Phylogenetic discrete character methods |
| Phylogeny distance matrix | Phylogenetic distance matrix methods |
| Phylogeny gene frequencies | Phylogenetic gene frequency methods |
| Phylogeny molecular sequence | Phylogenetic molecular sequence methods |
| Phylogeny tree drawing | Phylogenetic tree drawing methods |
| Protein 2d structure | Protein secondary structure |
| Protein 3d structure | Protein tertiary structure |
| Protein composition | Composition of protein sequences |
| Protein motifs | Protein motif searches |
| Protein mutation | Protein sequence mutation |
| Protein profiles | Protein profile generation and searching |
| Test | Testing tools, not for general use |
| Utils database creation | Database installation |
| Utils database indexing | Database indexing |
| Utils 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
References
- 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.
- Rice P, Bleasby A (1999). "EMBOSS: The European Molecular Biology Open Software Suite". Biochemist E-volution. 16 (6): 276–7. doi:10.1016/s0168-9525(00)02024-2. PMID 10827456.
- http://emboss.open-bio.org/html/dev/ch01s01.html
