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Emboss

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Title: Emboss  
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Emboss

EMBOSS 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.[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.

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 wordlwide 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]

Contents

  • EMBOSS application groups 1
  • See also 2
  • References 3
  • External links 4

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
  • EMBnet
  • USA Format - A format used to specify a sequence to be analysed.
  • Soaplab - A SOAP web service interface including EMBOSS
  • eBioX - An Open Source and free application with in-build support for most EMBOSS tools and plugins for other tools like Staden.
  • Geneious - A commercial application with a plugin for numerous EMBOSS tools
  • Genostar - Integration of some of EMBOSS tools in a graphical application

References

  1. ^ Rice P, Longden I, Bleasby A (2000). "EMBOSS: The European Molecular Biology Open Software Suite". Trends in Genetics 16 (6): 276–277.  
  2. ^ Rice P, Bleasby A (1999). "EMBOSS: The European Molecular Biology Open Software Suite". Biochemist e-volution. 
  3. ^ http://emboss.sourceforge.net/licence/

External links

  • Homepage of EMBOSS
  • Homepage of EMBnet
  • EMBOSS explorer - web-based GUI for EMBOSS
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