Sequences collections

The identification of peptides and proteins using MS information can be done in three different fashions (i) de novo sequencing, (ii) library searching, and (iii) sequence collection searching. 

SWISS-PROT, which can be classified as a computer-annotated sequence repository. The issues of completeness and redundancy are also described, and examples of specialized protein sequence collections are given. 

As with other stable isotope proxies, to infer paleoelevations or the presence/absence of a plateau, the isotope geochemist analyzing fossils has several options 1) Look high. Use a fossil sequence collected at high modern elevations (e.g., in a high mountain range... 

The gene for /3-galactosidase (lacZ) resides within a set of genes and regulatory DNA sequences collectively referred to as the lac operon (Fig. 7-2). 

Mammalian nuclear receptors regulate the expression or activation of target genes from promoter sequences that contain either a palindromic or a direct repeat DNA sequence collectively termed hormone response elements (HREs). Most nnclear receptors bind to HREs as either a homodimer... 

The two-dimensional H- H chemical shift correlated (2D NMR, COSY-45) data for isomeric 5P-cholestane-3a,7a,12a, 25-tetrol and 5P-cholestane-3a,7P, 12a,25-tetrol were acquired at a sweep width of 3200 Hz using a standard pulse sequence (collection of 256 free induction decays, FlDs) as described previously (28-30). A transform size of 2K x 2K data points was obtained after zerofilling. 

As mentioned in the introduction, there is now a considerable number of molecular biology and related databases available. While some are freely available, such as the DNA sequence collection EMBL [30] and GENBANK [18], others are only freely available to the academic community, such as the protein sequence database SWISS-PROT [15], and others are only available on subscription, such as the EST databases available from the company Incyte Genomics. Academics and pharmaceutical companies also have their own proprietary data which must be integrated into a system so that relationships with publicly available data can be found. 

Shown in Fig. 9 are four series of 2D IR spectra, using four different pulse sequences, collected for W(CO)6 solvated in hexane. Each series is generated... 

Complete genomic sequence of E. coli Complete genomic sequence of S. cerevisiae Complete genomic sequence of D. melanogaster Complete genomic sequences of vertebrate mitochondria Collection of primate Alu repeat sequences Collection of popular cloning vectors... 

The UniProt Archive (UniParc) provides a stable, comprehensive, nonredundant sequence collection by storing the complete body of publicly available protein sequence data. Although most protein sequence data are derived from the translation of DDBJ/EMBL/GenBank sequences, primary protein sequence data are also submitted directly to UniProt or derived from the PDB entries. The Archive also captures protein sequence data from other sources such as Ensemble, International Protein Index (IPI), NCBI-RefSeq, FlyBase, and WormBase. Each protein sequence is assigned to a unique UniParc identifier (UPI ) and represented only once in the Archive. In UniParc, the... 

The UniProt Reference databases (UniRel) provide nonredundant data collections based on the UniProtKB and UniParc, in order to obtain complete coverage of sequence space at several resolutions. UniRef databases (sequence collections clustered by sequence identity, for performing faster homology searches) are created as representative protein sequence databases witli high information content. 

The Universal Protein Resource (UniProt) provides the scientific community with a centralized, authoritative resource for protein sequences and functional information with three database components. (1) The UniProt Knowledgebase (UniProtKB), produced by a combination of automation and over 25 years of human curation, is the central protein sequence database with accurate, consistent, functional annotation and extensive cross-references. (2) The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from UniProtKB (including splice variants and isoforms) in order to obtain complete coverage of sequence space at several resolutions. The UniRef 100 database is particularly useful for Mass Spec identifications as it exposes known sequence variation and splice-form annotation contained in UniProtKB records. (3) The UniProt Archive (UniParc) provides a stable comprehensive sequence collection by storing the complete body of all publicly available protein sequence data. 

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