File Processing and Biological File Formats

SUMMARY

TITLE PERL TOPICS BIOLOGICAL TOPICS
Strings and DNA
  • Represent a DNA sequence using a string
  • Use substr to inspect a single character in a string
  • Concatentate strings using the dot operator
  • Identify the four nucleotides in DNA
  • Create complementary strings of nucleotides
    • Substitution
  • Use the s// operator
  • Describe the difference between DNA and RNA in terms of nucleotide content
  • Explain the process of transcription in general terms
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  • Distinguish between RNA and DNA by nucleotide content
  • Understand that there are several different types of RNA
  • Understand that an RNA transcript is created from a DNA template
    • Transliteration
  • Use the tr// operator
  • List the nucleotides used in DNA and RNA
  • Convert lowercase to uppercase and vice versa
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  • Know the difference between introns and exons
  • Recognize the difference between an RNA and DNA transcript
    • Pattern Matching
  • Use pattern matching with conditionals
  • Use the g option to force exhaustive pattern matching
  • Count using the pattern matching construct
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  • Know what codons are
  • Understand the relationship between RNA and amino acids
  • Know that multiple codons code for certain amino acids
    • Random Sequences
  • Use the seed functions to improve random number generation
  • Use the rand function to generate random numbers
  • Generate a random sequence of nucleotides
  • Use the substr and length functions to isolate portions of a string
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  • Understand that mutations are changes to DNA
  • Understand that mutations can have harmful, neutral, or beneficial effects for the organism
    • Transcribing and Translating Sequences
  • Use pattern matching to read a string three letters at a time
  • Use if-elsif-else construct to simulate translation
  • Use unless construct
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  • Know that codons correspond to amino acids
  • Know that amino acids have three and one letter abbreviations
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