Sentence examples for for protein identifiers from inspiring English sources

Specifically, we cast compartment prediction as multiple binary classification problems, where proteins of one nuclear body are labeled as positives and all proteins from other compartments are negatives (see Additional file 1 for protein identifiers and compartments when available).

Hence, we use the COGENT database [ 12] as our source for genome sequences, as it is constantly updated with new genomes and uses a consistent naming scheme for protein identifiers.

Several options to search pPCOMP are available, including a free text search applicable for all current protein identifiers, organism and strain names as well as the possibility to BLAST a sequence of interest against all proteins in the database.

We searched Swiss Prot Database for human NR and RTK and retrieved protein identifiers for 48 and 56 of them, respectively.

Users of the HAPPI web application software can search for PPIs using common protein identifiers.

"Protein1" and "Protein2" are the protein identifiers for the cross linked peptides.

The complete set of 914 orthologous sequences is listed in Additional file 2, Table S2 along with the designation of known or novel and the corresponding ensembl gene, transcript and protein identifiers for the dog, human and mouse orthologs.

Thus, instead of merging PPI information for any protein identifier stored in the source databases, the latter were selectively mined for PPIs exclusively between members of the as above defined reference human protein set.

Further, integration of interactions from multiple databases requires accurate annotations for the interactions such as valid protein identifiers and standardized terms for experimental description.

From our own experience, this is a highly demanding task, especially when it comes to viruses for which species, strains and protein identifiers have to be clearly defined, and because mature proteins are often not identified in viral polyprotein sequences.

To account for these difficulties we assigned protein identifiers to newt and zebrafish EST clones after BLASTx searches on TrEMBL and Swiss-Prot databases.