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When an animal's gene more closely matched a gene from a nonanimal than any other animals, the researchers took a closer look, using computational methods to determine whether the initial database search had missed something.
When the researchers scanned their database of DNA sequences from basil leaves and petunia flowers, they spotted a sequence that matched a gene implicated by another research group in producing the petunia's scent.
Out of these genes, 91% (21/23) matched a gene on the sequenced contigs at their expected location.
When multiple Agilent or Affymetrix probe sets from external data sets matched a gene in the gene signature, the probe set with the highest log2ratio standard deviation across samples was selected to represent the gene.
When multiple Agilent, Affymetrix or Illumina probe sets matched a gene in a gene signature, the probe set with the highest log2ratio standard deviation across samples was selected to represent the gene.
First, under the assumption that all tags that matched a gene represent transcription of some kind, we summed the average cpm of all tags from the sense strand, or separately, from the antisense strand (Additional file 1: Figure S6a).
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So researchers simply have to make artificial, double-stranded RNA that matches a gene they wish to investigate, and introduce it into a cell.
We defined AGC as the number of reads matching a gene multiplied by read length and divided by gene length.
A notable example of such a transfer is a catalase-encoding gene (Theba_0075) most closely matching a gene in Desulfitobacterium dichloroeliminans, a dehalo-respiring member of the Clostridia.
EST sequences matching a gene from these transcripts of interest were aligned (BLASTX) against the NCBI NR protein data set to verify best match to our EST.
Sensitivity score describes the percentage of probes in a probeset that match a gene and specificity score denotes how many other genes match the probeset and to how many probes within the probeset they match.
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matched a sequence
matched a record
matched a league
matched a quo
matched a program
matched a sample
matched a consensus
matched a team
matched a fuel-cost
matched a set
matched a video
matched a franchise
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matched a career
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matched a description
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matched a protein
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Justyna Jupowicz-Kozak
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