BISC 2539 Study Guide - Final Guide: Shotgun Sequencing, Pyrosequencing, Bioinformatics
14 Dec 2017
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Document Summary
Genome= complete set of dna in a single cell of an organism. How to obtain the sequence of a genomes: break genome into pieces, read each fragment, overlap fragments where they align, continue to overlap until all fragments used. How to join contigs= use paired end reads sequencing sequencing reactions in beads. Approaches for deducing the total polypeptide parts: open reading frame detection. Analyze genome sequence to predict mrna and polypeptide sequences. Look for sequences that indicate stop/start codons, gene length= open reading frames: direct evidence from cdna sequences. Analyze mrna cdna is only exons (expressed regions) The orf of the cdna should be continuous between the start/stop codons. Expressed sequence tags (est) used to determine 3" and 5" ends: predictions of binding sites. Looks for sequences promoters, binding: using polypeptide and dna. Blast program: predictions based on codon bias finding programs predicted to be sites, etc similarity. Degenerate= many codons can call for the same amino acid.
