Hands on exercise day2

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Hands on exercise day2

  1. 1. Hands on exercises Day - 2 Sucheta Tripathy
  2. 2. Input sequence: • Gene id: 127364 • Run Blast against PS V1.0 assembly • Generate fasta sequence file out of blast files using the following tool: http://imed.med.ucm.es/Tools/blast2fasta.html • Translate the sequence fasta files into protein sequences
  3. 3. Finding Motifs • Run a motif search using MEME (http://meme.sdsc.edu/meme4_5_0/intro.ht ml)
  4. 4. Codon Evolution • Synonymous and non-synonymous codon substitution. • dn/ds ratio calculation (With a pair of sequences) http://www.bork.embl.de/pal2nal/ [Score higher than 1 -> positive selection Score less than 1 -> neutral changes Score equal to one -> stabilizing selection

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