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DNA - Information Storage [GENOMICS]

Bioinformatics Learning Framework

Society Learning Goals Articles Sample Learning Objectives
DNA - Information Storage [GENOMICS]
Where are data about the genome found (e.g., nucleotide sequence, epigenomics) and how are they stored and accessed?
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  • Describe how nucleotide sequence data are represented (FASTA, FASTQ, GenBank).
  • Describe the nucleotide databases available at NCBI.
  • Describe how the NCBI nucleotide databases intersect with other nucleotide databases (EBI, DDBJ, UniProt, etc.).
  • Compare and contrast the data contained in different nucleotide databases.
  • Search for a sequence record in a nucleotide database with a given accession number.
  • Create a collection of nucleotide sequence records that meet a specified criterion (e.g., gene name or symbol).
  • Determine the DNA methylation state of a particular region of a genome.
  • Describe the types of metadata that accompany sequence data to make for useful biological interpretation (e.g. biological source, accession number, GeneID, journal articles, etc.).
How can bioinformatics tools be employed to analyze genetic information?
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  • Calculate the alignment score between two DNA sequences using a provided scoring matrix.
  • Perform a BLASTN search and interpret the results.
  • Explain the BLASTN algorithm for nucleotide sequence information.
  • Interpret the biological significance of an e-value.
  • Annotate a prokaryotic gene (derive a model).
  • Annotate a eukaryotic gene (derive a model).
  • Create and interpret a multiple sequence alignment (e.g., T-COFFEE, MUSCLE, etc.).
  • For a genomic region of interest (e.g., the neighborhood of a particular gene), use a genome browser to view nearby genes, transcription factor binding regions, epigenetic information, etc.
  • Describe Hidden Markov Models and how they can be used to assess motifs.

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