Casuarina SSR: Difference between revisions
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===Develop unigenes=== | ===Develop unigenes=== | ||
* TGICL is used | * TGICL is used | ||
* Contigs : | ** Param: Left to default | ||
* Singlets: | <pre> | ||
# -l miminum overlap length (default 40) | |||
# -M ignore lower-case masking in <fasta_db> sequences | |||
# -p minimum percent identity for overlaps <PID> (default 94) | |||
</pre> | |||
* Contigs : '''3947''' | |||
* Singlets: '''475''' | |||
* Unigenes: '''4422''' | |||
===Generate statistics=== | ===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 | |||
* Trimmed Sequences: '''4285''' | |||
=== | ===Mine for repeat motifs=== | ||
* Param: | |||
<pre> | |||
Definement of microsatellites (unit size / minimum number of repeats): (2/7) (3/5) (4/4) | |||
</pre> | |||
* Stat | |||
<pre> | |||
Total number of sequences examined: 4285 | |||
Total size of examined sequences (bp): 3253599 | |||
Total number of identified SSRs: 383 | |||
Number of SSR containing sequences: 347 | |||
Number of sequences containing more than 1 SSR: 30 | |||
Number of SSRs present in compound formation: 24 | |||
Distribution to different repeat type classes | |||
--------------------------------------------- | |||
Unit size Number of SSRs | |||
Di 217 | |||
Tri 141 | |||
Tetra 25 | |||
</pre> | |||
===Design Primers=== | ===Design Primers=== | ||
Latest revision as of 05:36, 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
- Trimmed Sequences: 4285
Mine for repeat motifs
- Param:
Definement of microsatellites (unit size / minimum number of repeats): (2/7) (3/5) (4/4)
- Stat
Total number of sequences examined: 4285 Total size of examined sequences (bp): 3253599 Total number of identified SSRs: 383 Number of SSR containing sequences: 347 Number of sequences containing more than 1 SSR: 30 Number of SSRs present in compound formation: 24 Distribution to different repeat type classes --------------------------------------------- Unit size Number of SSRs Di 217 Tri 141 Tetra 25