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A maximum likelihood tree was built from the curated alignments using PHYML [77].
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HMMs were built from highly curated multiple alignments of proteins thought to share the same function or to be members of the same protein family.
All of the proteins from the genome sequence were also searched against the Pfam [39] (release 20.0) HMMs (hmmpfam HMMER version 2.3.2, parameters: -E 0.1 –cut_ga) and TIGRFAMs [40] (release 6.0) built from highly curated multiple alignments of proteins thought to share the same function or to be members of the same family.
For comparing the feasibility and processing time between G.A.M.E. and its original CPU version, a natural product database (NPDB) was built from curating all of the known structures from the Dictionary of Natural Products (DNP) [32], the "ZINC natural products" subset of ZINC [33], and the Traditional Chinese Medicine Database [34].
Built from the ground up.
"They build from the language," he said.
Out of the remaining pathways, we built a selection curated by experts from the DC-THERA European network of excellence, where pathways were classified by their level of immunological relevance.
He built the MozCast and curates the Google Algorithm History, a journal of Google updates from 2002 to the present.
Unlike pre-built GG process networks, AN networks are built from input lists of network objects using the manually curated interaction database in MetaCore.
ELY built and curated the MRN protein multiple sequence alignments, helped with scoring missense substitutions, and helped to draft the manuscript.
These networks are built from heterogeneous data sources, including high-throughput interaction assays, curated protein-protein interaction databases, and conserved co-expression.
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