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This process is fully automated, but options for manual refinement of the results are available as well.
It allows automatic generation of a prototype code from the domain models and manual refinement of it.
Successive steps of manual refinement of all nine subunits using COOT [49] allowed tracing of more flexible regions as well as locating three sulfate ions at catalytic core domains., Multiple rounds of manual fitting followed by restrained and rigid body refinement in Refmac5 [48] reduced Rwork/Rfree to 0.31/0.34 and positioned all three Rrp4 proteins into density map.
In addition, manual refinement of the predicted gene models is on-going.
In addition, the use of pig cDNA sequences that have been completely sequenced accelerates the process of manual refinement of automated genome annotation.
Manual refinement of ab initio predicted and cross-species reconstructed sequences includes correcting wrongly predicted sequence regions, resolving sequencing problems and assembling myosins spread on several contigs.
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Shading and minor manual refinements of these aligned sequences were deduced using Genedoc (Nicholas et al. 1997).
Nonetheless, it provided useful output for further manual refinement to eliminate features of concern such as residual AT-rich strings and repeats.
Full alignments were built up using default settings of the Clustal program version 1.8 [ 53] followed by manual refinement to minimize the number of gaps.
Manual curation has become a luxury reserved for a few organisms and the majority of newly sequenced genomes only receive a single round of computational annotation with no additional manual refinement, therefore the utility of proteogenomics lies in its application at the primary stage of genome annotation to improve the quality and completeness of the automated genome annotation.
Models were optimized by using cycles of manual refinement with Coot [ 34] and refinement in Refmac5 [ 35], part of the CCP4 software suite [ 36], and in Phenix [ 37].
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