Non-Redundant database

S Henikoff, JG Henikoff, S Pietrokovski. BLOCKS+ A non-redundant database of protein alignment blocks derived from multiple compilations. Biomformatics 15 471-479, 1999. 

Swiss-Prot, TrEMBL Annotated non-redundant protein sequence database, TrEMBL is a computer-annotated supplement to Swiss-Prot. TrEMBL contains the translations of all coding sequences present in the EMBL Nucleotide Sequence Database which are no yet integrated into Swiss-Prot... 

High-speed identification from either PMF or MS/MS data can be achieved from non-redundant protein databases (Mann ef a/., 2001). These often include valuable annotations giving insight into functions of isolated and identified proteins. Many of these databases, such as NCBInr (National Centre for Biotechnology Information) and Swiss Prot (ExPASy Molecular Biology Server), can be used for protein identification. 

Without any doubt, mass spectrometry is now the most efficient way to identify proteins [75-78], The method is based on comparison of the data obtained from the mass spectrometry with those predicted for all the proteins contained in a database. The efficiency of the method results from the development of mass spectrometry into a rapid and sensitive method to analyse peptides and proteins and also from the availability of larger and larger databases. In October 2006, these databases contained more than 2400000 non-redundant sequences. Furthermore, the data obtained from genomic sequences after translation in the six lecture frames also can be used. The databases based on expressed sequence tags (ESTs) are another usable source for search. They are composed of sequences based on cDNA fast sequencing. They are limited to short lengths, about 300 bases, and contain many errors but they correspond to coding sequences. Despite their defects, they are very useful for identification of proteins by mass spectrometry [79]. 

Table II. Top 10 BLAST results for clone using the NCBI non-redundant (nr) peptide sequence database...

Bleasby, A. J. and Wootton, J. C., Construction of validated, non-redundant composite protein sequence databases. Protein Eng., 3, 153, 1990. 

Distribution of sequence identities between proteins in four genomes and their closest homologues in the Protein Databank for those sequences in genomes with homologues in the PDB. PSI-BLAST was used to search the non-redundant protein sequence database with a representative set of PDB sequences as queries. The program was run for four iterations, with a maximum expectation value of 0.0001 (see Chapter 2 for an... 

The second step was to gather orthologous sequences of BACE to define the family of sequences to which BACE belongs. We searched both the non-redundant protein sequence database at NCBI as well as the EST databases. The resulting alignment of BACE orthologues is shown in Figure 5.3... 

For many applications, such as protein identification or sequence similarity searches, it is necessary to use a database as complete and non-redundant as possible. SWISS-PROT, and to some extent TrEMBL, aim to... 

Pruitt, K. D., Tatusova, T and Maglott, D. R. (2005) NCBI Reference Sequence (RefSeq) a curated non-redundant sequence database of genomes, transcripts, and proteins. Nucleic Acid Res. 33, D501-D504. 

UniProt is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. UniProt is comprised of three components, each optimized for different uses. The UniProt Knowledgebase (UniProt) is the central access point for extensive curated protein information, including function, classification, and cross-reference. The UniProt Non-redundant Reference (UniRef) databases combine closely related sequences into a single record to speed searches. The UniProt Archive (UniParc) is a comprehensive repository, reflecting the history of all protein sequences. 

Database searches were performed against a non-redundant NCBI database using Mascot (Matrix Science, London, UK) selecting human and/or rodent species. Parent ion and fragment ion mass tolerances were both set at 0.6 Da. 

Very large numbers of non-redundant, reliable gene sequences, which are now available for several vertebrate species, allow higher levels of resolution than were previously possible, and prompted us to analyze their landscapes (two-dimensional distributions) in more detail. We focussed on human, where a nonredundant set of 10,218 genes was available from a well-curated human sequence database. We also studied the landscapes for three other vertebrates that are represented by large sequence databases, namely mouse, chicken and Xenopus (Cruveiller et al., 2004b). The warm-blooded vertebrate landscapes are adequately described by a structure of peaks and valleys along the landscapes crests, whereas the Xenopus landscape only shows a short crest with two peaks. 

Non-redundant merge of SWISS-PROT, PIR, PRF, and proteins derived from GenBank coding sequences and PDB atomic coordinates Subset of nr which is new or modified within the last 30 days The SWISS-PROT database... 

Note Abbreviations used align, alignment euk, eukaryotics DB, database genm, genome inti, international prok, prokaryotics FG, functional genomics GP genome project(s) chrom, chromosome(al) NR, non-redundant seq, sequence(s) phyl, phylogeny PT, phenotype(s) pub, public proj, project. 

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