Consensus coding sequences

Bachman, K.E., Papadopoulos, N., Vogelstein, B., Kinzler, K.W. and Velculescu, V.E. (2006) The consensus coding sequences of human breast and colorectal cancers. Science, 314, 268-274. 

Promoter sequences. In 1975, Pribnow pointed out46 that a series of six known promoters had a conserved 7-base sequence beginning six nucleotides upstream from the initiation site for transcription. Although this sequence varies somewhat from one promoter to another, it has been found in hundreds of E. coli promoters. This is called the -10 region, the Pribnow sequence, or Pribnow box (the last in recognition of the fact that people like to draw boxes around these special sequences). A typical 6-base consensus Pribnow sequence is 5-TATAAT as written for the coding strand, whose sequence corresponds to that of the rnRNA. Only three of these bases are highly... 

When predicting consensus structures, be aware that the quality of the prediction is limited by the quality of the input alignment. Nucleic acid alignments are generally more error-prone than protein alignments. For coding sequences it is sometimes preferable to back-translate a protein alignment. 

Each SOAP Web service is described in terms of Web Service Description Language (Booth and Liu 2007), which is a specification in XML. This enables data passed over the Web, say a sequence of characters such as CMRSGGCTRRYAC, to have its type specified according to an ontology, thus telling the code that that sequence of characters is a consensus DNA sequence rather than an author name or a geographical location. A RESTful Web service works in terms of HTTP requests and thus has potentially a less constrained syntax. 

These last factors also up-regulate hBD-2 secretion by the intestinal epithelial cell lineage Caco-2 stimulated with probiotic bacteria [176]. Although not yet demonstrated experimentally, mammalian cathelicidins may respond to inflammatory stimuli, since the 5 flanking sequences upstream of the peptide coding sequence have several potential consensus sequences for transcription factors involved in inflammatory response, sueh as NF-kB, NF-IL-6, acute-phase response factor and IFN-y response elements [147,170,177]. 

Special care is taken with the overlaps of the splice site consensuses and the coding sequence region. See the Concepts and Conventions section of the online documentation for details of the models and algorithms involved. GeneWise is available online. 

Translation of the consensus cDNA sequence using the standard genetic code results in a single open reading frame coding for human factor XII. The derived amino acid sequence agreed well... 

Figure 11 Diagrammatic representation of the tomato Bsubunit gene family members and related cDNAs in Arabidopsis thaliana. The four domains of the respective precursor proteins are coded as in Figure 4. The large triangles represent introns. Y s represent the position of glycosylation consensus sequences. Tomato Gene 1 is the fruit Bsubunit cDNA. Percentages underneath each mature and carboxyl domain indicate the respective identity to the mature and carboxyl domains of Tomato Gene 1.

Infergen (interferon alfacon-1 or consensus interferon) is an engineered interferon recently approved for the treatment of hepatitis C (Table 8.8). The development of infergen entailed initial sequence comparisons between a range of IFN-as. The product s amino acid sequence reflects the most frequently occurring amino acid residue in each corresponding position of these native interferons. A DNA sequence coding for the product was synthesized and inserted into E. coli. The recombinant product accumulates intracellularly as inclusion bodies. 

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