1. Hands on exercises Day - 2
Sucheta Tripathy

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. Finding Motifs
• Run a motif search using MEME
(http://meme.sdsc.edu/meme4_5_0/intro.ht
ml)

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