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In some cases, it is possible to manually resolve these ambiguities by using additional information not available to the assembler.
In an attempt to manually resolve this area, short (~30 bp) unique sequences within the trnS and cox2 genes were used to probe the sequence database for reads that extended from these two loci into the repeat region.
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Spurious mappings were manually resolved.
Regions with nucleotides represented as Ns were manually resolved by retrieving sequence information directly from the quality trimmed reads.
The resulting contigs were then manually resolved into a single contig using the de Bruijn graph of contigs.
In that case, the model composition interface provides a list of Warning Messages, to be manually resolved by the user.
Flags are manually resolved by annotators using controlled vocabulary or automatically resolved if the next data update does not trigger the same conflict.
Addresses were automatically geocoded (NavTeq 2006) to TigerLine files (U.S. Census Bureau 2009) and then manually resolved in a multistep process similar to that described by McElroy et al. (2003).
We then examined the functional annotation of these paralogous groups, verified the uniformity of their annotations and manually resolved any inconsistencies.
The tree was checked manually to resolve homoplasies.
Phylogenetic relationships among the complete mtDNA sequences were established using the reduced median network algorithm http://www.fluxus-engineering.com and the tree was checked manually to resolve homoplasies.
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