Sentence examples for rat protein database from inspiring English sources
Concatenated forward and reverse sequences from the NCBI Refseq rat protein database (updated 10.18.2006; 36,496 forward sequences) [50] were used for searching.
The IPI rat protein database (version 3.40, 40381 sequences, 20547209 residues) and its reversed complement were combined and used for database searches.
Protein identification using MS/MS raw data was performed with SEQUEST software (Thermo Finnigan) by searching against the Swiss-Prot rat protein database.
Database searches were performed on an in-house Mascot server (Matrix Science, London, UK) against IPI (International Protein Index) rat protein database.
To visualize compartment-specific sequence motifs, we analyzed all lysine acetylation sites from proteins localized to a particular subcellular compartment relative to the rat protein database using ice-Logo (Colaert et al., 2009).
The MS/MS data were searched against the IPI rat protein database with 10 ppm and 0.8 Da for MS and MS/MS tolerances, respectively, using the SEQUEST algorithm.
All searches were performed against an in-house rat database containing the entire rat RefSeq protein database (National Center for Biotechnology Information; www.ncbi.nlm.nih.gov; downloaded 01 March 2006) supplemented with sequences of potentially contaminating proteins, including human keratins, bovine serum albumin (BSA), and trypsin.
Expected numbers of proteins for each Rattus chromosome were taken from a count of protein accession numbers from the rat protein RefSeq database [ 33].
From the 4 full primary sequences of NNT (human, mouse, bovine and rat) available in the protein database, F215 is present in a highly conserved segment not part of the predicted NAD binding site (residues 229 259).
Protein identification was performed by searching the MS/MS spectra against rat protein sequences in the NCBInr database using a Mascot search engine (version 2.4.1).
Samples were searched against all rat and mouse entries in the protein database.
