Eukaryotic sequences

Use as a tool (see Note 1) for genome search and annotation that integrates microbial genome sequence data with most eukaryotic sequence data as well as viral and plasmid sequences (8). 

Eukaryotic sequences were suitably aligned, then one of them was used as a query to search for finished and unfinished prokaryotic genomes via a BLAST server. If several homologs were found in a single species, only the most similar one was chosen for alignment. In the basis of the BLAST hit, the annotated complete sequence was retrieved from the finished genome when available. 

Shapiro MB, Senapathy P (1987) RNA splice junctions of different classes of eukaryotes sequence statistics and functional implications in gene expression. Nucleic Acids Res 15 7155—7174... 

A bulged nucleotide occurs in a number of eukaryotic sequences at position 29.1, however. Nucleotides added relative to E. coli numbering are designated by decimal additions e.g., 44.1, 44.2. .. would indicate nucleotides added between E. coli positions 44 and 45. 

Gibbs has a large number of options and modes of operation (24). In this chapter we will concentrate on the subset of these options that are used for predicting TFBSs in cross-species data. The following examples illustrate the principles involved in computational detection of TFBS in prokaryotes, however, the principles are similar for the analysis of eukaryotic sequences. We will point out differences in the analysis of eukaryotic sequence data in the Note section (see Note 2). 

Saccharomyces cerevisiae 1996 12 Mb Yeast, the first eukaryote sequenced... 

The last of the critical eight aromatic rings is phenylalanine-82, totally invariant over all 60 eukaryotic sequences and the two bacterial cytochromes whose three-dimensional structures are known. It is found nested against the heme, closing the upper left of the heme crevice as shown in Fig. 6. Although this residue was formerly believed from the two-derivative, 2.8 A resolution electron density map of horse oxidized cytochrome to be swung out and away from the heme in ferricytochrome (12-1J ), the four-derivative, 2.0 A map of tuna ferricytochrome has revealed this to be incorrect (15). In both oxidation states, phenylalanine-82 appears to lie next to the heme, and the crevice remains "closed in the sense observed in Fig. 7. 

The widespread occurrence of polypurine polypyrimidine tracts in eukaryotic DNA suggests that these sequences may have a biological function. Analysis of eukaryotic sequence databases reveals thousands of polypurine polypyrimidine tracts, many with the potential for triplex formation. These polypurine regions of DNA can potentially influence biology in several ways. They could provide binding sites for regulatory proteins, influ-... 

The successful purification of eukaryotic sequence-specific DNA-binding proteins with the use of affinity chromatography as the critical step is no longer limited to the initial examples... 

Thns far, yeast has been nsed almost exclnsively to clone eukaryotic sequences. Sequences from a few bacteria have been cloned (7-9), and we have stably cloned and modified several complete bacterial genomes in yeast (4, 6, 10-13). To date, we have cloned whole genomes from mycoplasmas. 

In this review we will try to summarize the current knowledge of biochemistry and molecular biology of the OST from lower and higher eukaryotes. Sequence search in databases indicate also homologous proteins in archaea that may be involved in the A-glycosylation of these organisms. The reader is also referred to previous reviews dealing with this topic [28 31]. 

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