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That was the first mistake.In Ariane 5 the alignment function was redundant, but was not removed the second mistake.
Spots were matched using the alignment function of Progenesis SameSpots and Progenesis PG220 (version 2006; Nonlinear Dynamics, Durham, NC) matches were manually verified.
Multiple sequence alignment can be easily performed using the "alignment" function, which provides two widely adopted multiple sequence alignment program MUSCLE [ 9] and ClustalW [ 10] with a number of advanced parameters.
Of the contigs, 1355 (78%) of G. max's and 1053 (37%) of G. soja's were ordered and oriented to 20 soybean chromosomes (Schmutz et al. 2010) using the alignment function of FPC (Nelson and Soderlund 2009).
GenBank-deposited ORF predictions specifically for pleD from wOo, and cckA of wAlbB and wMel strains, were confirmed using the alignment function of CLC sequence viewer (version 6.9.1; http://CLCbio.com).
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Based on visual examination, total number of peaks and total intensity, one of the samples was selected as reference and all other ion intensity maps from rest of the samples were aligned to it using the 'Automatic Alignment' function in the software.
All the spot areas recognized by the automatic alignment function of the GenePix Pro were confirmed visually.
The pylogentetic tree was generated with the "Create Tree" function of CLC Main Workbench using the UPGMA algorithm with a bootstrap analysis of 100 replicates, based on an alignment of the HRP amino acid sequences using the "Create Alignment" function with the following settings: Gap open cost: 10.0, Gap extension cost: 1.0, End gap cost: as any other, Alignment: Very accurate (slow).
Deduced amino acid alignments were generated using the "create alignment" function of CLC-sequence viewer 6.9.1 based on the CLUSTALW alignment matrix/algorithm.
These alignments were then combined using the profile alignment function of ClustalX 1.83 [ 73].
Using the multiple alignment function of RSmatch, we generated a consensus structure for each structure group.
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