Sequence in databases

Databases Comparison of DNA and protein sequences obtained from unknown gene with known sequences in databases can facilitate gene identification. 

Once a peptide family has been sequenced, the next step is to overlap the available sequence information, in order to obtain the protein sequence. However, peptide sequences are more frequently used to identify proteins by searching the peptide sequences in databases. Several databases are available, and their utility... 

In order to trace (find, change, add, or delete) a segment in the database, the sequence in which the data arc read is important. Thus, the sequence of the hierarchical path is parent > child > siblings. The assignment of the data entities uses pointers. In our example, the hierarchical path to K is traced in Figure 5-fi. 

Having built a hidden Markov model for a particular family of proteins, it can then b< used to search a database. A score is computed for each sequence in the database anc those sequences that score significantly more than other sequences of a similar length ar( identified. This was demonstrated for two key families of proteins, globins and kinases ii the original paper [Krogh et al. 1994]. For the kinases, 296 sequences with a Z score abov<... 

The basic structural unit of these two-sheet p helix structures contains 18 amino acids, three in each p strand and six in each loop. A specific amino acid sequence pattern identifies this unit namely a double repeat of a nine-residue consensus sequence Gly-Gly-X-Gly-X-Asp-X-U-X where X is any amino acid and U is large, hydrophobic and frequently leucine. The first six residues form the loop and the last three form a p strand with the side chain of U involved in the hydrophobic packing of the two p sheets. The loops are stabilized by calcium ions which bind to the Asp residue (Figure S.28). This sequence pattern can be used to search for possible two-sheet p structures in databases of amino acid sequences of proteins of unknown structure. 

Three key areas are the organisation of knowledge in databases, sequence analysis, and structural bioinformatics. 

With the onset of genomic biology, there are now many sequences derived from genome sequencing projects that are too divergent to be considered species variants of known peptidases. Of the 54,124 sequences in the MEROPS database only 18,741 (34.6%) have been assigned to an identifier. 

Eng, J. K. McCormack, A. L. Yates, J. R. An approach to correlate tandem mass spectra data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 1994,5, 976-989. 

Once sufficient numbers of intrinsically disordered and ordered protein sequences were collected, it became possible to compare them directly. The sequences in these databases were examined for dilferences in amino acid composition, sequence attributes, and evolutionary characteristics. 

Three groups of disordered proteins have been assembled, with the groups defined by the experimental method used to characterize the lack of ordered structure. Because the focus has been on long regions of disorder, an identified disordered protein or region was not included in these groups if it failed to contain 40 or more consecutive residues. Disordered regions from otherwise ordered proteins as well as wholly disordered proteins were identified. Table I summarizes the collection of sequences in this database. 

Ulrich CM, Bigler J, Velicer CM et al. Searching expressed sequence tag databases discovery and confirmation of a common polymorphism in the thymidylate synthase gene. Cancer Epidemiol Biomarkers Prev 2000 9 1381-1385. 

The experimental MS/MS spectra are matched against theoretical spectra and cross correlation scores are calculated based on the extent to which the predicted and experimental spectra overlap.8 The higher cross correlation scores reflect a high level of matching of the experimental and predicted MS/MS spectra, and vice versa. The difference between a normalized cross correlation score and the next best match is reported as the (ACn) and indicates the quality of the top match in comparison to the next ranked sequences in the database.8... 

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