Casuarina SSR: Difference between revisions
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** Param: Trimmed off the <220bp | Trimmed off the N>5% | ** Param: Trimmed off the <220bp | Trimmed off the N>5% | ||
** ID Named | ** ID Named | ||
===Mine for repeat motifs=== | ===Mine for repeat motifs=== | ||
===Design Primers=== | ===Design Primers=== | ||
Revision as of 03:52, 29 December 2011
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
- Contigs :
- Singlets:
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