Sequence Alignment

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•  BLAST searches can identify similar sequences in different organisms

•  BLASTn allows nucleotide sequence alignment while BLASTp allows protein alignment

BLAST searches use an algorithm to compile similar sequences from a range of different organisms

  • BLAST stands for Basic Local Alignment Search Tool
  • Results are presented in order of relevance – based on the degree of match to a search sequence

BLAST searches can be used to compare either nucleic acid or protein sequences:

  • BLASTn compares nucleotide sequences to allow for DNA or RNA alignments
  • BLASTp compares amino acid sequences to allow for protein alignment

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•  Sequence alignment software allows comparison of sequences from different organisms

Certain software programs can display multiple sequences together to show the degree of similarity between them

  • This is called a sequence alignment and is commonly used to show the degree of relatedness between sequences
  • Protein sequences usually show more similarities than nucleotide sequences because of the degeneracy of the genetic code
    • I.e. Some codons code for the same amino acid, so different nucleotide sequences can code the same protein sequence

Multiple Alignment of a Protein Sequence from Various Species

multiple alignment

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•  Use of software to align two proteins

Clustal Omega is a free online tool that will align nuclotide or amino acid sequences for comparison

  • It can compare multiple (more than two) sequences at once
  • Sequence consensus can be colour coded in a Jalview applet found under ‘Result Summary’ (requires Java)

To construct a multiple alignment:

  • Change the input sequence type to the relevant form (DNA, RNA or protein)
  • Paste the relevant sequences into the provided space
  • Before each sequence designate a species name preceded by a forward arrow (e.g. '>Human’ or ‘>Chimpanzee’)
  • Alternatively, sequences can be saved as a document in plain text format (.txt) and then uploaded
  • When all sequences have been included, click ‘Submit’ (under step 3)

Below are plain text files that contain nucleotide and amino acid sequences for multiple alignment:

  • CHRNE  –  Cholinergic receptor epsilon (nicotinic) for various species (nucleotide sequence)
  • HBA  –  Haemoglobin alpha chain from various species (amino acid sequence)