Databases SwissProt

In the biosciences, a database is a curated repository of raw data containing annotations, further analysis, and links to other databases. Examples of databases are the SWISSPROT database for annotated protein sequences or the FlyBase database of genetic and molecular data for Drosophila melanogaster. 

Pasquier, C., Promponas, V., Palaios, G., Hamodrakas, J., and Hamodrakas, S. (1999). A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database the PRED-TMR algorithm. Protein Eng. 12, 381-385. 

Five unmatched masses 663.9700 1388.7100 1632.8100 2039.9800 2375.0400. The database searched was the SwissProt database cysteines were carbamidomethylated the peptide masses were monoisotopic the peptide mass error was <0.1 Da the protein molecular weight range was 1,000— 100,000 Da one missed cleavage was allowed. 

The EMBL in Heidelberg provides a multitude of services that can be hclprful Ah the molecular modeler. DSSF, HSSFt FSSP, FDBFINDER, PDBREPORT, and PDB SELECT are derived protein databases. They are based on data from the Protein Data Bank of 3D structures and the Swissprot database of LD protein sequences. The data and related software can be obtained vis anonymous FTP or, mote easily these days, via the WWW. 

As science has become increasingly specialized over the past two decades, so too has the area of bioinformatics. There are numerous specialized databases that deal with different aspects of biology. Some of these specialize in the area of proteins, while others specialize in the area of DNA. In general, these sites differ in two respects the general database(s) from which they draw information, and the parameters that they require the user to define to conduct the search. For instance, the AA Analysis database searches the more general SwissProt database to identify or group proteins on the basis... 

The proteins separated by SDS-PAGE with MWs ranging from 10,000 Da to 100,000 Da were identified as adenoviral proteins from the SwissProt database when searched against all taxonomy. The results were summarized in Table 19-7. 

Click on the link indicated by H next to the Protein-protein BLAST (blastp) to access a similar problem to determine the type of protein. Use the query sequence provided in the problem. This sequence was generated by translating a 4 exon gene from Drosophila. To determine the nature of this protein, run a blastp search against the Swissprot database as described in Subheading 2. The protein is similar to a number of phosphoglucomutases. 

Similar to protein-DNA interactions, protein-RNA interactions also perform vital roles in the cell including protein synthesis, viral replication, cellular defense and developmental regulation [145,146]. One major direction in the analysis of protein-RNA interactions is to identify proteins that bind RNA based on features derived from physio-chemical properties of the sequence. A number of published works have focused casting this problem as a binary classification problem using the support vector machines (SVM) classifier to identify proteins that bind RNA [33-35, 51]. Each of these works derived large data sets from the SwissProt database and applied the support vector machines classifier to discriminate protein sequences that bind RNA from all other sequences. Since sequence analysis techniques can identity homologous proteins as having similar function, most of these works reduced the redundancy of the data sets below a certain threshold <40% [35], < 25%... 

Figure 8.9. Output of a PASTA search, (a) Hit list from a PASTA search with human histidine triad (HIT) protein (SWISS-PROT P49789) as the query against the swissprot database. The search was performed using ktup = 1. (b) Optimal local alignment of the query to one of the database entries (marked by arrow in hit list) containing the sequence of rat galactose-1-phosphate uridylyltransferase (GalT). Although the sequence similarity is weak, these proteins have been shown to share structural similarity.

In our first example we use a low-performance mass spectrometer. Assuming that five peptides (m/z 729.86,818.95,1072.32,1253.49, and 1530.65) appear in the mass spectrum (e.g., as commonly observed, due to the ion-suppression effect we do not detect all tryptic peptides), the average masses are determined with 2000 ppm mass accuracy, and the search in the SwissProt database is restricted to the proteins of Homo sapiens, the MS-Fit searching tool of Protein Prospector [11] finds 114 entries that are more or less consistent with this data. The relevant section of the mass spectrum is shown in Fig. 2. Note that in this example no impurities complicate the spectrum. 

The mass differences in the b series reveal the presence of L/I followed by S in the sequence. This information is sufficient to attempt a sequence tag search. Searching the SwissProt database for H. sapiens proteins by entering m/z 1833.9 for the parent ion and 1108.5, 1021.5, and 908.4 for the b series fragments in the MS-Seq searching tool of Protein Prospector [11] turns up a single protein, human hemoglobin a subunit with primary accession number P69905. 

SwissProt database http //www.expasy.cb/sprot/sprot-top.html... 

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