Lecture 2: Sequence alignments

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Lecture 2Sequence alignments
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Unaligned sequences
Aligned sequences
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Unaligned vs. aligned
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Good alignments are critical for constructing
distance matrices and phylogenies
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Secondary structure of ribosomal RNA

• Complex pattern of short double-stranded stems,
  unpaired single-stranded loops and bubbles

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Alignments linked to secondary structure
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Secondary structure helix symbols in ARB
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The PT_SERVER

• Stands for positional tree server
• A different form of your sequence database which
  is necessary for faster search functions which
  are useful for sequence alignments and primer and
  probe design
• Saving your database does not affect your
  PT_SERVER, you must update this server
  independently
• You should only update the PT_SERVER when your
  database consists of well-aligned sequences

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Tutorial 2 objectives

• Become familiar with navigating ARB
• Build and update a PT_SERVER
• Import sequences into ARB
• Align sequences automatically in ARB
• Manually improve sequence alignments
• Align sequences using a web-based server (SINA)