Hence, as a second major contribution, following the work done by Cohen et al., we propose and make available a set of 32 manually crafted criteria (or test cases) comprising 2164 entries.
Then we checked the remaining sequences manually according to criteria made previously [ 46- 48].
Slides for p-HER2 were scored manually following the criteria of the Herceptest.
A manually specified energy criteria based off of computational alanine scanning (Kortemme et al., 2004) was used to identify co-located hot spots on a helix that provided a significant portion of the free energy of the helical interaction.
The eight sequenced Cymbidium cp genome sequences and two public orchid cp genomes were aligned using MAFFT version 5 [ 73] and five loci were adjusted manually according the criteria of reducing gaps.
This initial automated annotation was verified and edited manually by using criteria such as the presence of a ribosome-binding site, GC frame plot analysis and similarity to known protein-encoding sequences (CDS).
The results were verified and improved manually by using criteria such as the presence of a ribosome-binding site, GC frame plot analysis, and similarity to known protein-encoding sequences using the Sanger Artemis tool [ 76].
The results from 40 iterations of the algorithm were checked manually for two criteria: i) the result did not suggest a reversible reaction for a known irreversible reaction and ii) the added reaction(s) are known to occur in mouse.
To visualize the differential expression pattern, before Z value ranking, all gene ontology terms were further filtered manually with the criteria: the number of changed genes: >2; the number of measured genes: >10; the percent of changed genes: >5%; the percent of gene presented on the chip: >20%.
The singular values are always selected manually by some criterion, for example, the number of linear events in the analysis window (Oropeza and Sacchi 2011).
Instead, the authors screened manually for this criterion.
