protein_Alignment Virginia Bioinformatics Institute http://pathport.bioinformatics.vt.edu:6565/axis/services/msa http://pathport.vbi.vt.edu/services/wsdls/beta/msa.wsdl Wraps ClustalW program for multiple sequence alignment of protein sequences. It calculates the best match for the given sequences, and lines them up so that the identities, similarities and differences can be seen. protein_Alignment <s:arbitrarywsdl xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:wsdl>http://pathport.vbi.vt.edu/services/wsdls/beta/msa.wsdl</s:wsdl><s:operation>protein_Alignment</s:operation></s:arbitrarywsdl> Wraps ClustalW program for multiple sequence alignment of protein sequences. It calculates the best match for the given sequences, and lines them up so that the identities, similarities and differences can be seen. in0:sequence protein_AlignmentRequest List of protein sequences in fasta format. For example: >Protein sequence1 MFQAFPGDYDSGSRCSSSPSAESQYLSSVDSFGSPPTAAASQECAGLGEMPGSFVPTVTA >Protein sequence2 MFQAFPGDYDSGSRCSSSPSAESQYLSSVDSFGSPPTAAASQECAGLGEMPGSFVPTVTA false http://www.mygrid.org.uk/ontology#protein_sequence String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in1:outOrder protein_AlignmentRequest Output order. Select one of the following 2 options: ALIGNED | INPUT| false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in2:name protein_AlignmentRequest Optional parameter. Sequence names or IDs false http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter in3:gapOPenPenalty protein_AlignmentRequest Gap Open Penalty (Pairwise Alignment). For example 10.00 10.00 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in4:gapExtensionPenalty protein_AlignmentRequest Gap Extension Penalty (Pairwise Alignment). For example 0.1 0.1 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in5:mulgapOPenPenalty protein_AlignmentRequest Multiple Gap Open Penalty (Multiple Alignment). For example 10.00 10.00 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in6:mulgapExtensionPenalty protein_AlignmentRequest Multiple Gap Extension Penalty (Multiple Alignment). For example 0.2 0.2 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in7:distance protein_AlignmentRequest Gap Separation Distance. For example 4 4 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in8:divergence protein_AlignmentRequest Percent of divergence. For example 30 30 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in9:pairProteinMatrix protein_AlignmentRequest Protein Weight Matrix (Pairwise Alignment). Select one of the following options: blosum| pam| gonnet| id| gonnet false String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in10:multiProteinMatrix protein_AlignmentRequest Protein Weight Matrix (Multiple Alignment). Select one of the following options: blosum| pam| gonnet| id| gonnet false String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter protein_AlignmentReturn protein_AlignmentResponse Return a Multiple Sequence Alignment report in XML format. false http://www.mygrid.org.uk/ontology#multiple_sequence_alignment_report http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter http://www.mygrid.org.uk/ontology#global_aligning WSDL service