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Around 25% of the tags that matched to genes are in antisense orientation (Table 3).
Therefore, the resulting ortholog clusters had to be matched to genes.
The 52 unique sequence TDFs were matched to genes by BLAST searching the Arabidopsis thaliana genome (TAIR v.8).
A total of 97.8% of the sequences was matched to genes by Blast analysis against the refGene database.
There are also abundant reads that matched to genes for "lipid metabolism" (4,385 reads), such as fatty acid, glycerolipid, glyceropholipid, arachidonic acid, and linoleic acid metabolisms.
We introduce the subSeq R package, which instead subsamples sequencing reads with binomial sampling after they have been matched to genes and assembled into a count matrix.
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Microarray probes were matched to gene identifiers using the CDF array annotation (version 18) provided by the University of Michigan microarray© lab56.
These results are from analyses where the probes are matched to gene exons and using SNP proxies of eSNPs.
The most established computational approaches to function detection primarily depend on homology matching to genes with known functions utilizing programs such as FASTA [4] and PSI-BLAST [5].
These EST sequences are submitted to databases and compared to all other sequences in the databases to see if they match to genes whose function has been determined.
All EST matches to genes were required to have >80% coverage over the EST sequence.
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