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In fact, it was manually reconstructed from some of the millions of shreds of paper that panicked Stasi officials threw into garbage bags during the regime's final days in the fall of 1989.
The most parsimonious phylogenetic trees were manually reconstructed from the 20 haplogroup P1 sequences, as well as the five non-P1 complete mitogenomes to depict their position among published sequences [ 17, 28, 44, 52- 55, 80, 87, 107- 116].
Gene sequences were identified either by TBLASTN searches within the various species genome sequence projects using known ABAD/HSD10 amino acid sequences as queries or manually reconstructed from whole genome shotgun (WGS) traces through MEGABLAST searches.
Although most of the full-length ORFs in Table 1 were taken directly from the metagenome, several were manually reconstructed from fragmented genes identified in the assembly of the metagenomic dataset.
Whereas the algorithm-based sequences were produced using solely the coded data from two electronic sources, the 159 observed sequences were manually reconstructed from the medical records, which collect all patient information produced and documented by staff involved in patient care.
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Because not all known human metabolic pathways are included in HumanCyc and KEGG, we also considered a more recent human metabolic network, manually reconstructed by integrating genome annotation information from different databases and metabolic reaction information from specialist literature [38].
In order to gain understanding about the unique characteristics of this important pathogen, we manually reconstructed the metabolic network of M. tb in silico (iNJ661), from which we developed a model to compute perform computational analyses and interpret experimental data.
Then we submitted the pair-wise alignment to the HHrepID server to obtain an accurate alignment of the three PUR repeats, from which the multiple alignment of the six repeats from human and D. melanogaster Pur-α was manually reconstructed.
The host phylogeny was taken from the literature (Arias and Sheppard 2005; Raffiudin and Crozier 2007; Lo et al. 2010) from which a well-supported consensus tree was manually reconstructed.
A total of 240 intracortical connections were manually reconstructed within a common neuroanatomic framework, forming a cortico-cortical connectivity map that facilitates comparison of connections from different cortical targets.
If holes were located at the edge of the leaf, the missing edge was manually reconstructed.
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