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By mining the sequence reads, SSR-containing sequences can be identified.
The sequence search strategy devised, described below, was implemented for data mining the sequence homologues for structural superfamilies.
AD carried out the data mining, the sequence alignments, bioinformatic analysis and wrote the manuscript.
SXD and ADZ carried out the data mining, the sequence alignments, bioinformatic analysis and wrote the manuscript.
LS participated in the design of the study, the data mining, the sequence alignment and the bioinformatic analysis, and drafted the Methods section of the Manuscript.
Mining the sequence of the C. parvum genome has revealed that the only route to guanine nucleotides is via inosine-5′-monophosphate dehydrogenase (IMPDH).
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By mining the sequencing data, several abundant miRNAs were shown to be induced by low temperature treatment; the expression profiles of these miRNAs were confirmed using northern hybridization.
The present study contributes to our knowledge on fungal DyPs by mining the sequenced genome of P. ostreatus for enzymes of this new peroxidase family.
Further, we mined the sequence data of 17 plant species to identify and similarly annotate 133 full length AGOs.
Novartis scientists, led by Dr Rino Rappuoli, mined the sequence data to discover dozens of novel proteins that could serve as potential antigens.
Because EMS typically causes G-to-A or C-to-T base pair changes, and because we assumed the causative mutation would be homozygous in the population, we mined the sequencing data for homozygous G-to-A or C-to-T base pair changes and found a total of 8 homozygous, EMS-related mutations not present in our wild-type sequence that clustered on the long arm of chromosome 2 (Table 2).
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