Clustal and other MSA tools

Clustal

There are two versions of Clustal produced by its authors: Clustal 2 (also called ClustalW2) and Clustal Omega. Both provide multiple sequence alignment, although Clustal Omega currently only works on protein sequences (www.clustal.org). Clustal Omega has a publication at http://dx.doi.org/10.1038/msb.2011.75. Clustal 2 comes in command-line (ClustalW) and GUI (ClustalX) versions. A publication for these two versions (W and X) can be found at http://dx.doi.org/10.1093/bioinformatics/btm404.

The EBI runs a web service which utilises ClustalW called ClustalW2 (for Clustal version 2) and another for Clustal Omega, and defines that software as a general purpose multiple sequence alignment program for DNA or proteins (http://www.ebi.ac.uk/Tools/msa/clustalw2/).

All of these were modelled as follows (annotation labels removed for brevity):

Class: Clustal
SubClassOf:
software,
‘achieves objective’ some ‘Multiple sequence alignment’

Class: ‘Clustal Omega’
SubClassOf:
Clustal

Class: ‘Clustal Omega 1.1’
SubClassOf:
‘Clustal Omega’,
‘has documentation’ value “http://dx.doi.org/10.1038/msb.2011.75“,
‘has interface’ only ‘Command Line Interface’

Class: ClustalW
SubClassOf:
Clustal

Class: ‘ClustalW 2.1’
SubClassOf:
ClustalW,
‘has documentation’ value “http://dx.doi.org/10.1093/bioinformatics/btm404”,
‘has interface’ only ‘Command Line Interface’

Class: ClustalX
SubClassOf:
Clustal

Class: ‘ClustalX 2.1’
SubClassOf:
ClustalX,
‘has documentation’ value “http://dx.doi.org/10.1093/bioinformatics/btm404”,
‘has interface’ only ‘Graphical User Interface’

Class: ‘EBI Clustal Omega Web Tool’
SubClassOf:
‘Clustal’

Class: ‘EBI Clustal W2 Web Tool’
SubClassOf:
‘Clustal’

 

MUSCLE

MUSCLE is similar to both Clustal and TCoffee in that there is the core software which is accessed both directly and via Web tools.

Documentation (such as papers) and information about owning organisations have been added.

TCoffee

TCoffee is similar to both Clustal and MUSCLE in that there is the core software which is accessed both directly and via Web tools. As such, the following hierarchy has been made:

Documentation (such as papers) and information about owning organisations have been added. Of special note is the two-step interface provided by the core TCoffee software. There was no way to model ordering of interfaces, so the fact that it begins on the command line and the continues as a GUI is modelled as follows:

Class: 'CRG TCoffee 9.02.r1228'
    Annotations: 
        label "CRG TCoffee 9.02.r1228"@en,
        definition "The initial interface is via the command line. Depending on the options and inputs provided at the command line, an appropriate alignment takes place and is then presented to the user via a Graphical User Interface.",
        creator "Allyson Lister"    
    SubClassOf: 
        'CRG TCoffee',
        'is specified output of' some 
            ('Software publishing process'
             and ('has participant' value 'Centre for Genomic Regulation (CRG) of Barcelona')),
        'has interface' some 'Graphical User Interface',
        'has interface' some 'Command Line Interface'

Future Work

Please note that versions have not been added (although the appropriate software classes have been created) as we are in the middle of a discussion as to how to handle version numbers. A different blog post will deal with the issue of software interfacing/accessing other software. Once complete, such an interface would allow statements such as “EBI Clustal W2 Web Tool accesses ClustalW 2.1”. Ownership of the software (organisations) should also be provided.

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