In this study a commercially available software, Chip Inspector was used, which also employs a re-annotation of probe sequences but uses in house annotation and does not employ probe set definition [12].
CLI refers to the in house annotation.
For C. parapsilosis, contig sequences were obtained from the Sanger Institute, and a Broad Institute annotation supplemented with in-house annotations was used.
The different kinds of sequence identifiers included in the database are shown in Figure 3. Performing in-house annotations allowed us to discard any probe that could be associated with more than one gene.
Protein features were supplied by APPRIS (29), a database that houses annotations of protein structural and functional data and information from cross-species conservation for the human genome.
Atlantic salmon BAC sequences surrounding the hemoglobin gene clusters were annotated using our in-house annotation pipeline described above.
These were week-long intensive jamborees to annotate cDNA and genomic sequence with our in-house annotation tools (Otterlace/ZMap), aimed mainly at the Principal Investigators (PI's) of interested groups.
The software uses PubNub for real-time annotations, Elixir/Phoenix lean API on the backend, Apollo to the React JS front-end and in-house annotation libraries.
For Sulfobacillus thermosulfidooxidans strain Cutipay, predicted proteome sequence was obtained from an in-house annotation of its genome (GenBank ID: ALWJ01000000) as described previously (Travisany et al. [2012]).
We discuss the combined use of IIXTM, the ThermoML Archive, and an in-house annotation database to efficiently search information on ionic compounds and to derive structure-property relationships in advancing application-oriented selection of supporting electrolytes and RTIL media.
Thus, probe sets mapping to the same gene id represent redundant probe sets according to Affymetrix' in-house annotation pipeline.
