Biochemistry 2280A Lecture Notes - Lecture 23: Contig, Stop Codon, Start Codon

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Sequence gap: can be closed by completing the sequence of clones in the library, computer scans for clones that are found in 2 different contigs. Physical gaps: gaps that are not sequence gaps, not represented by clones in the original library (entire library, physical gaps can be filled in by using pcr. To identify the physical gap you will do 82 pcr reactions (40 contigs: primer 1 with each of all the other primers (except primer 2) If 2 contigs are adjacent they will yield a pcr product: band is shown on the gel, sequence this dna and you fill in the physical gap. Types of info the genome contains: expressed regions, protein encoding genes trnas rrnas. Transcriptional regulatory sequences: promoters, terminators: ori of replication, nucleosome positioning elements (euks) How are protein encoding sequences annotated in the bacterial genome: what are the features of a protein encoding gene, promoter. Stop codon--- the 3 above are collectively called open reading frame-

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