Exercises:

• Are you able to run tfm ?
• Can you find a program to:
  • Display multiple alignments.
  • Find ORFs (Open Reading Frames).
  • Translate a sequence.
  • Find restriction enzyme sites
  • Find the isoelectric point of a protein.
  • Do global alignments.

Are you able to run:-

• patmatdb: Search a protein sequence with motif
• patmatmotifs: Search a PROSITE motif database with a protein database
• remap: search rebase for enzyme
  

Database installation

• prosextract : prosite.dat is needed
• Rebaseextract: rebase files are needed

Working on multiple files

• @file operator
• writing batch scripts
  

other variables

• -sbegin sequence begin position
• -send sequence end position
• -sreverse reverse complement the sequence
• -slower change sequence to lower case
• -supper change sequence to upper case
• -osformat output sequence format
• -help show help
• -options ask for optional parameters
• -auto run silently (for use in scripts, e.g. perl)