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Sequences were aligned at the protein level using MUSCLE version 3.8.31 with default options [ 38] with minor manual corrections to eliminate spurious amino acid replacements generated by the alignment procedure.
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Although the initial clustering of shotgun sequences was refined in the alignment procedure by Phrap [ 23], a small number of SNPs still mapped to two distinct genomic regions.
The retention times determined before alignment using the alignment procedure described by Eq. 4 are summarised in Table 2.
However, TS-AMIR improves this precision by focusing on the geometry of the structures in the alignment procedure at the residue level.
In general, most of the GC-FID fingerprints were characterized by correlation coefficients that were higher than 0.8 after the alignment procedure.
The alignment procedure finds the protein reading frames encoded by the sequences that make up the isolate.
The alignment procedure should allow alignment of conserved regions separated by large gaps, but also of relatively divergent sequences as most of the curated gene families are multi-domain containing proteins.
After the alignment procedure, the involvement of the AI genes with drought tolerance was tested by selective genotyping.
The alignment procedure is described and results for the alignment precision and position resolution are reported.
In Section 3 we describe the phantoms used in our experiments and the alignment procedure.
Diverse conformations within 20 kcal/mol energy range were generated and submitted to the alignment procedure.
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