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runnableitem.xml
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<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<ns4:runnableItem xmlns:ns2="bibiserv:de.unibi.techfak.bibiserv.cms.microhtml" xmlns:ns3="bibiserv:de.unibi.techfak.bibiserv.cms.minihtml" xmlns:ns4="bibiserv:de.unibi.techfak.bibiserv.cms" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="dialign" xsi:schemaLocation="bibiserv:de.unibi.techfak.bibiserv.cms http://bibiserv.techfak.uni-bielefeld.de/xsd/bibiserv2/BiBiServAbstraction.xsd">
<ns4:name xml:lang="en">Dialign</ns4:name>
<ns4:shortDescription xml:lang="en">DIALIGN is a multiple alignment program based on segment-to-segment comparison.</ns4:shortDescription>
<ns4:description xml:lang="en">DIALIGN is a software program for multiple sequence alignment
developed by <ns2:a href="http://www.gobics.de/burkhard/">Burkhard
Morgenstern</ns2:a><ns2:em>et al.</ns2:em>. <ns2:p>While standard alignment methods rely
on comparing <ns2:em>single</ns2:em> residues and imposing <ns2:em>gap
penalties</ns2:em>, DIALIGN constructs pairwise and multiple alignments by comparing
entire <ns2:em>segments</ns2:em> of the sequences. No gap penalty is used. This approach
can be used for both global and local alignment, but it is particularly successful in
situations where sequences share only <ns2:em>local</ns2:em> homologies.</ns2:p>
<ns2:p>The latest version of the program, <ns2:a href="http://dialign-tx.gobics.de/"
>DIALIGN-TX</ns2:a>, is described in <ns2:a
href="http://www.almob.org/content/3/1/6/abstract/">Subramanian <ns2:em>et
al.</ns2:em> (2008), <ns2:em>Algorithms Mol. Biol.</ns2:em> 3:6</ns2:a>. A web
server for this program is available at <ns2:a href="http://www.gobics.de">Goettingen
Bioinformatics Compute Server (GOBICS)</ns2:a>. A web server for multiple alignment
with user-defined constraints (anchor points) as described by <ns2:a
href="http://www.almob.org/content/1/1/6/abstract">Morgenstern <ns2:em>et
al.</ns2:em> (2006), <ns2:em>Algorithms Mol. Biol.</ns2:em> 1:6</ns2:a> is also
available through GOBICS.</ns2:p>
<ns2:p>During the last few years, DIALIGN has been successfully used by many researchers to
<ns2:a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/16/10/948">align
genomic sequences</ns2:a>; some break-through discoveries have been made based on
these alignments. We set up a
<ns2:a href="http://dialign.gobics.de/chaos-dialign-submission">WWW server for multiple
alignment of genomic sequences</ns2:a> using Mike Brudno's program CHAOS and DIALIGN
at GOBICS, see
<ns2:a href="http://nar.oxfordjournals.org/cgi/content/abstract/32/suppl_2/W41">Brudno
<ns2:em>et al.</ns2:em> (2004), <ns2:em>Nuc. Acids. Res.</ns2:em>
32:W41-W44</ns2:a>.</ns2:p>
</ns4:description>
<ns4:toolTipText xml:lang="en">Dialign - multiple alignment program</ns4:toolTipText>
<ns4:keywords xml:lang="en">multiple alignment segment-to-segment dna rna protein</ns4:keywords>
<ns4:responsibleAuthor>
<ns4:firstname>Burkhard</ns4:firstname>
<ns4:lastname>Morgenstern</ns4:lastname>
<ns4:organisation>Universitaet Goettingen</ns4:organisation>
<ns4:email>[email protected]</ns4:email>
</ns4:responsibleAuthor>
<ns4:author>
<ns4:firstname>Said</ns4:firstname>
<ns4:lastname>Abdeddaim</ns4:lastname>
<ns4:email>[email protected]</ns4:email>
</ns4:author>
<ns4:support>
<ns4:firstname>BiBiServ</ns4:firstname>
<ns4:lastname>Mitarbeiter</ns4:lastname>
<ns4:email>[email protected]</ns4:email>
</ns4:support>
<ns4:references>
<ns4:reference>@article{MOR:2004,
author={Morgenstern,B.},
title={DIALIGN: Multiple DNA and Protein Sequence Alignment at BiBiServ},
year=2004,
URL={http://nar.oxfordjournals.org/cgi/content/full/32/suppl_2/W33},
journal={Nucleic Acids Research},
number={32},
pages={W33-W36}
}</ns4:reference>
<ns4:reference>@article{SUB:KAU:MOR:2008,
author={Subramanian,A.R. and Kaufmann,M. and Morgenstern,B.},
title={DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment.}
year=2008,
URL={http://www.almob.org/content/3/1/6/abstract},
journal={Algorithms for Molecular Biology}
number={3}
}</ns4:reference>
<ns4:reference>@article{MOR:PRO:POEH:STA:2006,
author={Morgenstern,B. and Prohaska,S.J. and Poehler,D. and Stadler,P.F.},
title={Multiple sequence alignment with user-defined anchor points},
year={2006},
URL={http://www.almob.org/content/1/1/6},
journal={Algorithms for Molecular Biology},
number={1}
}</ns4:reference>
<ns4:reference>@article{POEH:WER:STE:MOR:2005,
author={Poehler,D. and Wernera,N. and Steinkamp,R. and Morgenstern,B.},
title={Multiple Alignment of Genomic Sequences using CHAOS, DIALIGN and ABC},
year={2005},
URL={http://nar.oxfordjournals.org/cgi/content/abstract/33/suppl_2/W532},
journal={Nucleic Acids Research},
number={33},
pages={W532-W534}
}</ns4:reference>
<ns4:reference>@article{SCHMO:NIE:KAU:MOR:2004,
author={Schmollinger,M. and Nieselt,K. and Kaufmann,M. and Morgenstern,B.},
title={DIALIGN P: Fast pair-wise and multiple sequence alignment using parallel processors.},
year={2004},
URL={http://www.biomedcentral.com/1471-2105/5/128/abstract},
journal={BMC Bioinformatics},
number={5},
pages={128}
}</ns4:reference>
</ns4:references>
<ns4:executable>
<ns4:version>2.2.1</ns4:version>
<ns4:execInfo>
<ns4:executableType>docker</ns4:executableType>
<ns4:image>dialign</ns4:image>
<ns4:path>/dialign</ns4:path>
<ns4:callingInformation></ns4:callingInformation>
</ns4:execInfo>
<ns4:input id="dialign_input_aa_sequences">
<ns4:name xml:lang="en">aa_sequences</ns4:name>
<ns4:shortDescription xml:lang="en">aminoacid sequences</ns4:shortDescription>
<ns4:description xml:lang="en">A set of amino acid sequences to be aligned.</ns4:description>
<ns4:type>Fasta_AA_Multi</ns4:type>
<ns4:handling>FILE</ns4:handling>
<ns4:example>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</ns4:example>
</ns4:input>
<ns4:input id="dialign_input_dna_sequences">
<ns4:name xml:lang="en">dna_sequences</ns4:name>
<ns4:shortDescription xml:lang="en">deoxyribonucleic acid sequences</ns4:shortDescription>
<ns4:description xml:lang="en">Deoxyribonucleic acid sequences to be aligned.</ns4:description>
<ns4:type>Fasta_DNA_Multi</ns4:type>
<ns4:handling>FILE</ns4:handling>
<ns4:example>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</ns4:example>
</ns4:input>
<ns4:input id="dialign_input_rna_sequences">
<ns4:name xml:lang="en">rna_sequences</ns4:name>
<ns4:shortDescription xml:lang="en">ribonucleic acid sequences</ns4:shortDescription>
<ns4:description xml:lang="en">Ribonucleic acid sequences to be aligned.</ns4:description>
<ns4:type>Fasta_RNA_Multi</ns4:type>
<ns4:handling>FILE</ns4:handling>
<ns4:example>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</ns4:example>
</ns4:input>
<ns4:output id="dialign_output_aaalignment">
<ns4:name xml:lang="en">AA alignment</ns4:name>
<ns4:shortDescription xml:lang="en">multiples amino acid alignment</ns4:shortDescription>
<ns4:description xml:lang="en">Multiples Amino Acid Alignment.</ns4:description>
<ns4:type>Fasta_AA_Alignment</ns4:type>
<ns4:handling>FILE</ns4:handling>
<ns4:option>-fa -fn </ns4:option>
<ns4:example></ns4:example>
</ns4:output>
<ns4:output id="dialign_output_dnaalignment">
<ns4:name xml:lang="en">DNA alignment</ns4:name>
<ns4:shortDescription xml:lang="en">multiples deoxyribonucleic acid alignment</ns4:shortDescription>
<ns4:description xml:lang="en">Multiples deoxyribonucleic acid alignment.</ns4:description>
<ns4:type>Fasta_DNA_Alignment</ns4:type>
<ns4:handling>FILE</ns4:handling>
<ns4:option>-fa -fn </ns4:option>
<ns4:example></ns4:example>
</ns4:output>
<ns4:output id="dialign_output_rnaalignment">
<ns4:name xml:lang="en">RNA alignment</ns4:name>
<ns4:shortDescription xml:lang="en">multiples ribonucleic acid alignment</ns4:shortDescription>
<ns4:description xml:lang="en">Multiples ribonucleic acid alignment.</ns4:description>
<ns4:type>Fasta_RNA_Alignment</ns4:type>
<ns4:handling>FILE</ns4:handling>
<ns4:option>-fa -fn </ns4:option>
<ns4:example></ns4:example>
</ns4:output>
<ns4:outputfile id="dialign_outputfile_aaalignment">
<ns4:name xml:lang="en">Output as Custom Format</ns4:name>
<ns4:filename>dialign_output_aaalignment.FILE</ns4:filename>
<ns4:contenttype>text/plain</ns4:contenttype>
</ns4:outputfile>
<ns4:outputfile id="dialign_outputfile_dnaalignment">
<ns4:name xml:lang="en">Output as Custom Format</ns4:name>
<ns4:filename>dialign_output_dnaalignment.FILE</ns4:filename>
<ns4:contenttype>text/plain</ns4:contenttype>
</ns4:outputfile>
<ns4:outputfile id="dialign_outputfile_rnaalignment">
<ns4:name xml:lang="en">Output as Custom Format</ns4:name>
<ns4:filename>dialign_output_rnaalignment.FILE</ns4:filename>
<ns4:contenttype>text/plain</ns4:contenttype>
</ns4:outputfile>
<ns4:param id="dialign_param_threshold">
<ns4:name xml:lang="en">threshold</ns4:name>
<ns4:shortDescription xml:lang="en">Threshold for fragments weights</ns4:shortDescription>
<ns4:description xml:lang="en">
<ns2:p>As described in our papers, DIALIGN constructs alignments from gapfree pairs of segments of the sequences.
Such segment pairs are referred to as <ns2:em>diagonals</ns2:em>.</ns2:p>
<ns2:p>Every possible diagonal is given a so-called weight reflecting the degree of similarity among the two segments involved.
The overall score of an alignment ist then defined as the sum of weights of the diagonals it consists of and the program
tries to find an alignment with maximum score -- in other words: the program tries to find a consistent collection of diagonals
with maximum sum of weights. This novel scoring scheme for alignments is the basic difference between DIALIGN and
other global or local alignment methods. Note that DIALIGN does not employ any kind of gap penalty.</ns2:p>
<ns2:p>It is possible to use a threshold T for the quality of the diagonals. In this case, diagonals are considered only if their <ns2:em>weights</ns2:em>
exceed this threshold, and regions of lower similarity are ignored.</ns2:p>
<ns2:p>In the first version of the program (DIALIGN 1), this threshold was in many situations absolutely necessary to obtain meaningful alignments.
By contrast, DIALIGN 2 should produce reasonable alignments without a threshold, i.e. with T = 0. This is the most important difference
between DIALIGN 2 and the first version of the program.</ns2:p>
<ns2:p>Nevertheless, it is still possible to use a threshold T, so it is up to the user to experience with this option.</ns2:p>
</ns4:description>
<ns4:type>int</ns4:type>
<ns4:option>-thr </ns4:option>
<ns4:defaultValue>0</ns4:defaultValue>
<ns4:min included="true">0.0</ns4:min>
<ns4:max included="true">10.0</ns4:max>
<ns4:guiElement>INPUTTEXT</ns4:guiElement>
</ns4:param>
<ns4:enumParam maxoccurs="1" minoccurs="1" id="dialign_enumparam_nucleicacidsequencehandling">
<ns4:name xml:lang="en">nucleic acid sequence handling</ns4:name>
<ns4:shortDescription xml:lang="en">nucleic acid sequence handling</ns4:shortDescription>
<ns4:description xml:lang="en">If (possibly) coding nucleic acid sequences are to be aligned, DIALIGN optionally translates the compared `nucleic acid segments' to `peptide segments' according to the genetic code -- without (necessarily) presupposing any of the three possible reading frames, so all three of them get checked for significant similarity. In this case, the similarity among segments will be assessed on the `peptide level' rather than on the `nucleic acid level'. We strongly recommend this option if nucleic acid sequences are expected to contain protein coding regions, as it will significantly increase the sensitivity of the alignment procedure in such cases.</ns4:description>
<ns4:type>string</ns4:type>
<ns4:values>
<ns4:key>dialign_enumparam_nucleicacidsequencehandling_key0</ns4:key>
<ns4:value>-n </ns4:value>
<ns4:name xml:lang="en">nucleic acid without translation</ns4:name>
</ns4:values>
<ns4:values>
<ns4:key>dialign_enumparam_nucleicacidsequencehandling_key1</ns4:key>
<ns4:value>-nt </ns4:value>
<ns4:name xml:lang="en">nucleic acid with translation</ns4:name>
</ns4:values>
<ns4:guiElement>SELECTONERADIO</ns4:guiElement>
</ns4:enumParam>
<ns4:function id="dialign_function_aa">
<ns4:name xml:lang="en">AA alignment</ns4:name>
<ns4:shortDescription xml:lang="en">multiples amino acid alignment</ns4:shortDescription>
<ns4:inputref ref="dialign_input_aa_sequences"/>
<ns4:outputref ref="dialign_output_aaalignment"/>
<ns4:outputfileref ref="dialign_outputfile_aaalignment"/>
<ns4:paramGroup id="dialign_paramgroup_for_dialign_function_aa">
<ns4:description xml:lang="en"/>
<ns4:paramref ref="dialign_param_threshold"/>
</ns4:paramGroup>
<ns4:paramAndInputOutputOrder>
<ns4:reference>dialign_param_threshold</ns4:reference>
<ns4:reference>dialign_output_aaalignment</ns4:reference>
<ns4:reference>dialign_input_aa_sequences</ns4:reference>
</ns4:paramAndInputOutputOrder>
<ns4:example>
<ns4:name>Dialign (AA) example</ns4:name>
<ns4:prop idref="dialign_input_aa_sequences">PkhUTDINCkxEVEFQQ0xGU0RHU1BRS0FBWVZMV0RRVElMUVFESVRQTFBTSEVUSFNBUUtHRUxMQUxJ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</ns4:prop>
</ns4:example>
</ns4:function>
<ns4:function id="dialign_function_dna">
<ns4:name xml:lang="en">DNA alignment</ns4:name>
<ns4:shortDescription xml:lang="en">multiples deoxyribonucleic acid alignment</ns4:shortDescription>
<ns4:description xml:lang="en"/>
<ns4:inputref ref="dialign_input_dna_sequences"/>
<ns4:outputref ref="dialign_output_dnaalignment"/>
<ns4:outputfileref ref="dialign_outputfile_dnaalignment"/>
<ns4:paramGroup id="dialign_paramgroup_nasequencehandling">
<ns4:name xml:lang="en">na sequencehandling</ns4:name>
<ns4:shortDescription xml:lang="en"></ns4:shortDescription>
<ns4:description xml:lang="en"/>
<ns4:paramref ref="dialign_param_threshold"/>
<ns4:paramref ref="dialign_enumparam_nucleicacidsequencehandling"/>
</ns4:paramGroup>
<ns4:paramAndInputOutputOrder>
<ns4:reference>dialign_param_threshold</ns4:reference>
<ns4:reference>dialign_enumparam_nucleicacidsequencehandling</ns4:reference>
<ns4:reference>dialign_output_dnaalignment</ns4:reference>
<ns4:reference>dialign_input_dna_sequences</ns4:reference>
</ns4:paramAndInputOutputOrder>
<ns4:example>
<ns4:name>Dialign (DNA) example</ns4:name>
<ns4:prop idref="dialign_input_dna_sequences">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</ns4:prop>
<ns4:prop idref="dialign_enumparam_nucleicacidsequencehandling">dialign_enumparam_nucleicacidsequencehandling_key0</ns4:prop>
</ns4:example>
<ns4:example>
<ns4:name>Dialign (DNA) example 2</ns4:name>
<ns4:prop idref="dialign_input_dna_sequences">PnRlc3RzZXF1ZW5jZTENCkFDR1RHQ0dhVENHQ1RHQUNHQUdDQVRHQ0FUR0NUR0NBVEdDQVRHQ0FUQ0dBVEdDQVRDR0FUR0cNCj50ZXN0c2VxdWVuY2UyDQpBQ0FHQVRDR0FUQ0FUR0NBVEdDQVRHQ0FUQ0dBVENHVEFDR0FUR0NBVEdDVEFHQ0dUQUNDQUFB</ns4:prop>
<ns4:prop idref="dialign_enumparam_nucleicacidsequencehandling">dialign_enumparam_nucleicacidsequencehandling_key1</ns4:prop>
</ns4:example>
</ns4:function>
<ns4:function id="dialign_function_rna">
<ns4:name xml:lang="en">RNA alignment</ns4:name>
<ns4:shortDescription xml:lang="en">multiples ribonucleic acid alignment</ns4:shortDescription>
<ns4:description xml:lang="en"/>
<ns4:inputref ref="dialign_input_rna_sequences"/>
<ns4:outputref ref="dialign_output_rnaalignment"/>
<ns4:outputfileref ref="dialign_outputfile_rnaalignment"/>
<ns4:paramGroup id="dialign_paramgroup_for_dialign_function_rna">
<ns4:paramref ref="dialign_param_threshold"/>
<ns4:paramref ref="dialign_enumparam_nucleicacidsequencehandling"/>
</ns4:paramGroup>
<ns4:paramAndInputOutputOrder>
<ns4:reference>dialign_param_threshold</ns4:reference>
<ns4:reference>dialign_enumparam_nucleicacidsequencehandling</ns4:reference>
<ns4:reference>dialign_output_rnaalignment</ns4:reference>
<ns4:reference>dialign_input_rna_sequences</ns4:reference>
</ns4:paramAndInputOutputOrder>
<ns4:example>
<ns4:name>Dialign (RNA) example 1</ns4:name>
<ns4:prop idref="dialign_input_rna_sequences">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</ns4:prop>
<ns4:prop idref="dialign_enumparam_nucleicacidsequencehandling">dialign_enumparam_nucleicacidsequencehandling_key0</ns4:prop>
</ns4:example>
</ns4:function>
</ns4:executable>
<ns4:view type="submission" id="dialign_view_id">
<ns4:title xml:lang="en">Dialign Submission</ns4:title>
<ns4:customContent xml:lang="en"/>
</ns4:view>
<ns4:view type="webservice" id="dialign_view_webservice">
<ns4:title xml:lang="en">Dialign WebService</ns4:title>
<ns4:customContent xml:lang="en"/>
</ns4:view>
<ns4:view type="download" id="dialign_view_download">
<ns4:title xml:lang="en">Dialign Download</ns4:title>
<ns4:customContent xml:lang="en">
Dialign is a command line tool. That means there's no graphical user interface, you have to run it
from the command line.
<ns2:ul>
<ns2:li>Download the archive that fit your system.</ns2:li>
<ns2:li>Unzip the archive</ns2:li>
<ns2:li>Open a commandline and change into the unpacked directory.</ns2:li>
<ns2:li>Set DIALIGN2_DIR environment variable
<ns2:ul>
<ns2:li>Windows : set DIALIGN2_DIR=dialign2_dir</ns2:li>
<ns2:li>OSX : export DIALIGN2_DIR=dialign2_dir</ns2:li>
</ns2:ul>
</ns2:li>
<ns2:li>Run Dialign typing <ns2:em>dialign2-2.exe</ns2:em> (Windows) or
<ns2:em>./dialign2-2</ns2:em> (OSX) to get an usage help.
</ns2:li>
</ns2:ul>
</ns4:customContent>
</ns4:view>
<ns4:manual id="dialign_manual">
<ns4:introductoryText xml:lang="en">This manual describes all parameters, input and output data supported by this Dialign online service. The variation and count of
parameters, the parameter range and input/ output types can differ from the standalone used program.</ns4:introductoryText>
</ns4:manual>
</ns4:runnableItem>