Sentence examples for we were annotating from inspiring English sources

As we were annotating the P. sneebia and P. rettgeri genome sequences (see "Annotation methods" section below), we noticed several instances of sequential open reading frames (ORFs) that were annotated with the same predicted function and whose combined length equaled the size of genes with the same functional annotation in other bacteria.

As we are annotating TF and TC genes in maize and millet, which are C4 plants, it is interesting to know whether some of the TF and TC genes we identified are related to C4 photosynthesis or kranz anatomy development.

Because we are annotating species for which there are no model organism databases or reference gene set and we do not restrict our annotation to proteins from UniProtKB, biocurators may also add gene product record pages using accessions from NCBI if there is no UniProtKB record available or in cases where the protein record is not appropriate (e.g. functional RNAs).

The unique sequences we identified were annotated against the PlnTFDB [ 30], a recently developed database of transcription factor families for 22 plant species, using the BLASTx program.

Among the 20224 protein sequences of Homo sapiens we collected, 639 were annotated as the RNA-binding proteins according to the Cellular Component of Gene Ontology (GO 0003723, RNA binding, downloaded from BioMart, Additional file 4: Table S3).

We excluded ESTs that were annotated as mitochondrial libraries, tumour libraries, or multiple tissues.

Last, we excluded genes that were annotated as pseudogenes by TAIR (http://www.arabidopsis.org/).org/

Once sequences were annotated we used SPIDEY [ 44] to locate the coordinates on the appropriate contig.

For each of the cases so identified, we confirmed that they were annotated as mitochondrial or plastid sequences in NCBI GenBank.

As a control, we randomized which genes were annotated as disease orthologs, keeping the same total number of disease gene orthologs.

In this way we ensured that they were annotated in rather detailed GO terms, and therefore the attempt to get GO-DAG consistent predictions would be sensible.