Hands on exercises Day - 2

Sucheta Tripathy

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

Finding Motifs

• Run a motif search using MEME (http://meme.sdsc.edu/meme4_5_0/intro.html)

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 changesScore equal to one -> stabilizing selection