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In some instances, manual prediction of the complete coding region revealed strong similarity to human proteins which was not detected using the incomplete or fragmented models.
The basic method used to identify cytokines involves obtaining their sequence structures and functions by manual prediction [ 1], which can yield small-scale data.
Given the repetitive nature of this genome, as is the case for many other facultative or "recently" acquired intracellular endosymbionts, many of the gaps were flanked by repetitive regions or had them near the gaps, and manual prediction of primers avoiding repetitive sequence was time consuming.
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In this way, nine additional sequences were added as "manual" predictions to the list of candidates, giving rise to several predicted clusters of miRNAs (Figure 2 and Data S1).
As new technologies develop, new types of experimental datasets will become available and should be integrated into the computational and manual gene prediction process and analysis pipelines.
The main outputs of the Highway Development and Management Manual [18] include prediction of pavement performance and maintenance, road improvement effects, user costs and benefits, estimates of environmental effects, standard economic indicators etc.
The ploidy and contamination values were chosen based on manual confirmation and prediction made by ASCAT [ 25] on SNP 6.0 data of the same samples.
Current gene annotation and protein functional annotations are the result of both manual curation and prediction based upon machine-learning tools such as GenemarkS [ 8], RAST [ 9] and various homology-based methods such as FASTA [ 10].
Human ZF gene predictions for clusters 19.6 and 19.12 were derived by manual curation of predictions from NCBI RefSeq 25, ENSEMBL release 50, and the dedicated LLNL ZF annotation web resource [ 1].
The manual curation of predictions for three selected proteins confirms their high quality and precision as many predictions already have strong experimental support in the literature.
(iv) CURATEDMODELS: extrinsic predictions manually annotated for manual correction of merged or split predictions.
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