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By Michael Gribskov, John Devereux (eds.)

Covers the fundamental desktop analyses used for brand spanking new DNA sequences and makes an attempt to supply the researcher with the required heritage to be able to comprehend and use successfully those programs.

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CODING REGION IDENTIFICATION The coding region is defined as the region that is translated by ribosomes into a polypeptide. The coding region is delimited by sequences that function in the initiation and termination of transcription and translation. Eukaryotic genes, however, are commonly organized as exons and introns and hence may comprise several disjoint ORFs. 04 AGTGTCCA A C Flgure 29: Possible eukaryotic termination signal. Base frequencies for 70 sequences were determined by McLauchlan et al.

GGGAAGTGCAGAGGTAGCTCAGGCCAGATCAGTTTGATCCACTGCTCCA 273 274 143 87 75 ......... + ......... + ......... + ......... + .......... + ......... + Figure 15: GCG GelAssemble contig report. This display shows bases 2501 to 3000 of the contig E022ubah. Each sequence fragment is shown on a separate line with its name and the direction in which it was sequenced (as indicated by< or>) to the left. The position of the rightmost base of each fragment is given on the right.

CODING REGION IDENTIFICATION 39 The Stop Codon The second hallmark of a protein coding region is the termination or stop codon. Three stop codons, UAA, UAG, and UGA, suffice for all protein coding regions. A preference for the use ofUAG and UGA is observed in genes from organisms that have a high GC content In polycistronic genes, are-initiation event may occur immediately distal to the stop of the preceding coding region. When re-initiation is observed, the initiation codon is usually preceded by a termination codon within 10 bases, and the following initiation codon may actually overlap the termination codon.

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