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Article
Open AccessExhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes
Upstream open reading frames (uORFs) are present in the 5′-untranslated regions of many eukaryotic mRNAs, and some peptides encoded by these regions play important regulatory roles in controlling main ORF (mOR...
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Article
Open AccessComprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA
Upstream open reading frames (uORFs) in the 5′-untranslated regions (5′-UTRs) of certain eukaryotic mRNAs encode evolutionarily conserved functional peptides, such as cis-acting regulatory peptides that contro...
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Article
Open AccessExploring functionally related enzymes using radially distributed properties of active sites around the reacting points of bound ligands
Structural genomics approaches, particularly those solving the 3D structures of many proteins with unknown functions, have increased the desire for structure-based function predictions. However, prediction of ...
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Article
CIPRO 2.5: Ciona intestinalis Protein Database - a unique integrated repository of large-scale omics data, bioinformatic analyses, and curated annotation, with ability for user rating and comments
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Article
Open AccessImproved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations
The draft genome sequence of the ascidian Ciona intestinalis, along with associated gene models, has been a valuable research resource. However, recently accumulated expressed sequence tag (EST)/cDNA data have re...
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Article
Standardized Phylogenetic Tree: A Reference to Discover Functional Evolution
Functional evolution is often driven by positive natural selection. Although it is thought to be rare in evolution at the molecular level, its effects may be observed as the accelerated evolutionary rates. The...
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Article
Open AccessThe genome sequence and structure of rice chromosome 1
The rice species Oryza sativa is considered to be a model plant because of its small genome size, extensive genetic map, relative ease of transformation and synteny with other cereal crops1,2,3,4. Here we report ...
