Based on sequence match significance and frequencies within each set of organ libraries, genes hypothesized to be strongly responsive (42 total) within male medaka brain, liver, or testis were semi-quantitatively screened with replicate cDNA nylon membrane arrays.
Based on sequence match, we identified two putative PPREs in NHE1 and three putative PPREs in MnSOD promoter sequences.
Expert manual annotation of InterPro entries with GO terms enables users to infer function, process or subcellular information for uncharacterized sequences based on sequence matches to predictive models.
Mapping of array probe identifiers to reference transcriptome identifiers was based on sequence matches using BLASTN with an E-value cutoff of 1E-05.
Because of their small size, TFBS motifs are likely to appear throughout the genome frequently by chance, and it is difficult to determine which are likely to be functional based on sequence matches alone.
When we considered data from human and chimpanzee iPSCs together, without excluding probes based on sequence matches to the chimpanzee genome, all chimpanzee lines in the panel had pluripotency scores slightly below the pluripotency threshold.
The functional assignment of sequences from captured metagenomes was also carried out in MG-RAST based on sequence similarity matches with different databases along with SEED database where reads were annotated with different subsystems (E-value of 10−5).
The separation based on sequence relatedness is matched by separation of gene functions, since all known members of the TPS-g subfamily produce acyclic products.
For both the nLSU and COX1 data, outgroups were chosen based on closest sequence matches in the public databases, while for nSSU outgroups were chosen based on previous analyses.
Retrieval systems based on sequence similarity, description matches or microarray positions are also included, as well as browsing by species, experimental process, and annotation.
