Casuarina SSR

New SSRs Pipeline Target

• Designing Cross species EST SSRs from Casuarina
• Author: Ashok Kulkarni and Rajkumar
• Timeline
  • Designing Primers: DEC 2011
  • Oligo synthesis  : JAN 2012
  • Standardisation and Validation  : MAR 2010
  • Manuscript  : JUN 2010

Scientific Assumptions

EST SSRs are supposedly conserved across species therefore higher species transferability is expected

Strategy

• C. glauca ESTs
• Develop unigenes
• Generate statistics
• Filter the sequence
• Mine for repeat motifs
• Design Primers

Implementation

C. glauca ESTs

• Total Number of ESTs: 34897
• Total number of C. glauca ESTs: 34805

Develop unigenes

• TGICL is used
  • Param: Left to default

# -l miminum overlap length (default 40)
# -M ignore lower-case masking in <fasta_db> sequences
# -p minimum percent identity for overlaps <PID> (default 94)

• Contigs : 3947
• Singlets: 475
• Unigenes: 4422

Generate statistics

• Distribution of length in contigs:
• Distribution of length in singlets:
• Final number of sequence
  • Param: Trimmed off the <220bp | Trimmed off the N>5%
  • ID Named