Sequences accuracy

D. J. States, D. Botstein. Molecular sequence accuracy and the analysis of protein coding regions. Proc Natl Acad Sci USA. 1991, 88, 5518-5522. 

Another measure of DNA sequencing accuracy is the maximal correct read length of contiguous sequence that does not contain fhune shifts and wrong... 

This entry gives an overview of the fundamentals of DNA sequencing by CAE, jxCAE, and four-color laser-induced fluorescence (LIE) detection, as well as some major factors (sieving matrix, sample preparation, electric field strength, etc.) influencing the sequencing accuracy and efficiency. 

However, interpretation of, or even obtaining, the mass spectrum of a peptide can be difficult, and many techniques have been introduced to overcome such difficulties. These techniques include modifying the side chains in the peptide and protecting the N- and C-terminals by special groups. Despite many advances made by these approaches, it is not always easy to read the sequence from the mass spectrum because some amide bond cleavages are less easy than others and give little information. To overcome this problem, tandem mass spectrometry has been applied to this dry approach to peptide sequencing with considerable success. Further, electrospray ionization has been used to determine the molecular masses of proteins and peptides with unprecedented accuracy. 

Attempts have also been made at predicting the secondary stmcture of proteins from the propensities for residues to occur in the a-helix or the P-sheet (23). However, the assignment of secondary stmcture for a residue only has an average accuracy of about 60%. A better success rate (70%) is achieved when multiple-aligned sequences having high sequence similarity are available. 

Figure 9 Relative accuracy of comparative models. Upper left panel, comparison of homologous structures that share 40% sequence identity. Upper right panel, conformations of ileal lipid-binding protein that satisfy the NMR restraints set equally well. Lower left panel, comparison of two independently determined X-ray structures of interleukin 1(3. Lower right panel, comparison of the X-ray and NMR structures of erabutoxin. The figure was prepared using the program MOLSCRIPT [236].

Eortunately, a 3D model does not have to be absolutely perfect to be helpful in biology, as demonstrated by the applications listed above. However, the type of question that can be addressed with a particular model does depend on the model s accuracy. At the low end of the accuracy spectrum, there are models that are based on less than 25% sequence identity and have sometimes less than 50% of their atoms within 3.5 A of their correct positions. However, such models still have the correct fold, and even knowing only the fold of a protein is frequently sufficient to predict its approximate biochemical function. More specifically, only nine out of 80 fold families known in 1994 contained proteins (domains) that were not in the same functional class, although 32% of all protein structures belonged to one of the nine superfolds [229]. Models in this low range of accuracy combined with model evaluation can be used for confirming or rejecting a match between remotely related proteins [9,58]. 

In the middle of the accuracy spectrum are the models based on approximately 35% sequence identity, corresponding to 85% of the Ca atoms modeled within 3.5 A of their correct positions. Eortunately, the active and binding sites are frequently more conserved... 

The most important general lesson is that there are hydrophobic transmembrane helices, the positions of which within the amino acid sequence can be predicted with reasonable accuracy. This applies both to the single transmembrane-spanning helix within the H polypeptide chain of the reaction center and the five transmembrane helices of the L and M chains that... 

X-ray structures are determined at different levels of resolution. At low resolution only the shape of the molecule is obtained, whereas at high resolution most atomic positions can be determined to a high degree of accuracy. At medium resolution the fold of the polypeptide chain is usually correctly revealed as well as the approximate positions of the side chains, including those at the active site. The quality of the final three-dimensional model of the protein depends on the resolution of the x-ray data and on the degree of refinement. In a highly refined structure, with an R value less than 0.20 at a resolution around 2.0 A, the estimated errors in atomic positions are around 0.1 A to 0.2 A, provided the amino acid sequence is known. 

The pulses are used to transmit deviation data from 0° to 90° with a 45, 22.5, 11.25, etc., sequence binary code of 10 bits. What is the transmission accuracy Give the binary number for 27.4°. 

A 10-bit digital system uses the sequence 180, 90, 45, 22.5, etc., to transmit the azimuth value. What is the accuracy of the transmission Give the binary numbers for S-23-E by excess, default and nearest. 

So efficient is the automated dideoxy method that sequences up to 1100 nucleotides in length, with a throughput of up to 19,000 bases per hour, can be sequenced with 98% accuracy. After a decade of work, preliminary sequence information for the entire human genome of 2.9 billion base pairs was announced early in 2001- Remarkably, our genome appears to contain only about 30,000 genes, less than one-third the previously predicted number and only twice the number found in the common roundworm. 

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