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Automatically picked particles were manually verified using a correspondence analysis based method (Shaikh et al., 2008b).

All fragmentation spectra were manually verified using the criteria as described by Mann et al [48].

In silico predicted genomic sequences were manually verified using EST sequences (if possible).

The quality of reconstruction and 3D views were manually verified using DataViewer software (Skyscan).

All peptide sequences were manually verified using Analyst software with Bioanalyst (Applied Biosystems/MDS Sciex).

The predicted gene models were manually verified using BLASTX searches against the protein databases Uniprot [ 82] and NCBI-nr [ 83].

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A mtDNA COI haplotype network for H. armigera was constructed manually and verified using the program TCS, version 1.13 [ 59].

Amino acid sequences were aligned with those inferred from previously characterised mt genomes for species of Strongylida (i.e., An. duodenale, Ne. americanus and Co. oncophora) and C. elegans using Clustal W [ 57], adjusted manually and verified using BioEdit v.7.0.3 [ 58].

The initial alignment was adjusted manually and verified using Harmony3 (J. Shi, unpublished), which matches observed substitution frequency in the alignment with predicted substitution frequency from standard and environment specific substitution tables.

HPV genotyping profiles are manually interpreted and verified using the HPV reference guide provided with each test kit.

Orthologous HPTs in the three Bordetella genomes were manually confirmed using ACT [ 51], and alignments were verified using cross_match [ 52] and ClustalW [ 53].

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