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23 <title>Multiple Sequence Alignment Web Service</title>
26 <strong>Multiple Sequence Alignment Web Services</strong>
28 Multiple sequence alignment services are accessed from the <strong>Alignment</strong>
29 submenu of the Alignment Window's <strong>Web Service</strong> menu.
30 When an entry from one of these menus is selected, either the
31 currently selected residues, or the whole sequence set (if there is
32 no selection or only one sequence is selected) will be submitted for
33 multiple sequence alignment.
35 <p>There are two kinds of multiple sequence alignment operations
38 <li><em>alignment</em> - where a new alignment is constructed
40 <li><em>realignment</em> - where any aligned sequences will be
41 used by the service to construct a profile based alignment of the
42 remaining unaligned sequences</li>
44 <strong>JABAWS Alignment services</strong>
45 <br> Most alignment services are provided by the
46 <a href="JABAWS.html">JABAWS framework</a>, which allows you to
47 customise the precise parameters used when running each alignment
48 program. In addition to the 'Default settings', you may choose from a
49 range of alignment preset settings, or create your own using the
50 <a href="webServicesParams.html">'Edit Settings And Run ..' dialog
54 <strong>Alignment programs supported by JABAWS</strong>. <br />Versions
55 shown are those bundled with JABAWS 2.2 - if you are using a
56 different server, check its home page to find out which versions are
59 <li><a href="http://www.clustal.org/omega">Clustal Omega</a> (version 1.2.4)</li>
60 <li><a href="http://www.clustal.org/clustal2">ClustalW</a> (version 2.1)</li>
61 <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a> (version 7.310)</li>
62 <li><a href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31)</li>
63 <li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">T-coffee</a> (version 11.00.8cbe486)</li>
64 <li><a href="http://probcons.stanford.edu/">Probcons</a> (version 1.12)</li>
65 <li><a href="http://msaprobs.sourceforge.net/">MSAProbs</a> (version 0.9.7)</li>
66 <li><a href="http://sourceforge.net/projects/glprobs/">GLProbs</a> (version 0.9.7)</li>
71 <strong>Multiple Alignments of Sequences with hidden
72 columns</strong><br> Multiple alignment services are 'column
73 separable' analysis operations. If the input contains <a
74 href="../features/hiddenRegions.html">hidden columns</a> then
75 each visible segment of the input sequence set will be submitted for
76 alignment separately, and the results concatenated (with the hidden
77 regions preserved) once all alignment functions have completed. Each
78 sub-job's state is reported in its own tab:
81 <strong>Multiple Multiple Sequence Alignment sub jobs
82 running at once</strong>
86 <img src="multimafftjbs.gif" align="centre">