Casuarina SSR: Difference between revisions
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| Line 40: | Line 40: | ||
===Generate statistics=== | ===Generate statistics=== | ||
* Final number of sequence | * Final number of sequence | ||
** Param: Trimmed off the <220bp | Trimmed off the N>20% | ** Param: Trimmed off the <220bp | Trimmed off the N>20% | ||
** ID Named | ** ID Named | ||
* Distribution of length in contigs: 220-500: 546 | 500-1000: 3119 | 1000-1500: 529 | >1500: 98 | |||
===Mine for repeat motifs=== | ===Mine for repeat motifs=== | ||
===Design Primers=== | ===Design Primers=== | ||
Revision as of 05:08, 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
- 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
- Final number of sequence
- Param: Trimmed off the <220bp | Trimmed off the N>20%
- ID Named
- Distribution of length in contigs: 220-500: 546 | 500-1000: 3119 | 1000-1500: 529 | >1500: 98