New PDF release: Sequence Analysis in Molecular Biology. Treasure Trove or

By Gunnar Von Heijne

ISBN-10: 0127251308

ISBN-13: 9780127251301

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Extra resources for Sequence Analysis in Molecular Biology. Treasure Trove or Trivial Pursuit

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Experimental Background As for the eukaryotic promoters, no algorithm for finding eukaryotic terminators has yet been published, and the sequence determinants are not at all well understood. A major complication is that termination proper usually takes place a considerable distance downstream from the final mature 3' terminus of the RNA; hence any patterns found in the R N A are likely to be involved in posttranscriptional processing events (endonucleolytic cleavage and poly(A) addition) rather than in termination per se.

Theoretical Analyses The panoply of different regulatory sequences in the eukaryotic promoters has made theoretical analysis difficult, since only a few examples of any given signal are known. The T A T A box is well estab­ lished, however, and, as shown in Fig. 5, is embedded in a region of relatively low A T content (Nussinov et al, 1986; Bucher and Trifonov, 1986). The CCAAT box is much less distinct (not shown), but a second TATA-like region appears around position —275 in both mammalian and invertebrate sequences.

Throughout this section, it has been taken for granted that the initial aligning of the sequences is uncomplicated, and this is indeed the case when one is dealing with signals as distinct as the E. coli promoters. It would nevertheless be nice to have a general alignment algorithm that could be used to detect weaker signals without any prior knowledge of what to expect. A method that promises to do just this, given only a very approximate initial alignment, has been devised by Galas et al (1985).

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Sequence Analysis in Molecular Biology. Treasure Trove or Trivial Pursuit by Gunnar Von Heijne


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