EMBOSS
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'''EMBOSS''' is an acronym for '''E'''uropean '''M'''olecular '''B'''iology '''O'''pen '''S'''oftware '''S'''uite. EMBOSS is a free Open Source software analysis package specially developed for the needs of the [[molecular biology]] and [[bioinformatics]] user community.<ref name=Rice2000>{{cite journal |author=Rice P, Longden I, Bleasby A |title=[http://dx.doi.org/10.1016/S0168-9525(00)02024-2 EMBOSS: The European Molecular Biology Open Software Suite] |journal=Trends in Genetics |volume=16 |issue=6 |pages=276–277 |year=2000}}</ref> 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 application groups==
{| class="wikitable"
|-
!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 tree drawing methods
|-
|Phylogeny tree drawing || Phylogenetic molecular sequence 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.
==References==
<references/>
==External links==
*[http://emboss.sourceforge.net Homepage of EMBOSS]
*[http://www.embnet.org Homepage of [[EMBnet]]]
*[http://embossgui.sourceforge.net/ EMBOSS explorer] - web-based GUI for EMBOSS
[[Category:Free science software]]
[[Category:Bioinformatics]]
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