Friday, 18th of December 2009 at 01:19:02 PMFeb 13,2009
Taxonomy of the Species in Consideration:
Kingdom: Metazoa
Phylum: Echinodermata
Class: Echinoidea
Order: Echinoida
Family: Echinodermata
Genus:Heliocidarus
Heliocidarus tuberculata, also called the brown Sea Urchin is commonly found attached to the rock substrate either singularly or in clusters in rock pools and crevices within the lower tidal zone. It has a circular hard outer covering that is symmetrical on the radial axis. The main features that distinguish this from similar species are its brown colour and its spines, which are blunt at the tip.
Heliocidarus erythrogramma, another species of the same genus Heliocidarus has pointed spine tips and can be purple, green or white in colour.
Objective of Mini Group Project #1
To Conduct assembly of the preprocessed and cleaned EST sequences obtained from the above two species, using ESTPiper and to summarize the results.
Experimental Procedure:
- Cleaned EST Sequences of Heliocidarus erythrogramma and Heliocidarus tuberculata were given separately as input to the De novo assembler available on the ESTPiper. All the Advanced options were set to default.
- From the assembly output files, the lengths of EST sequences, number of EST sequences in the contigs, lengths of contigs belonging to both the species, were obtained by writing Perl Scripts to do the same.
- The output values obtained from the perl scripts were read into R and length distribution of EST sequences, distribution of number of sequences in the contigs, distribution of lengths of contigs were obtained in the form of Histograms.
Summary from Assembly:
| H. erythrogramma | H. tuberculata | |
Total input ESTs |
8599
|
8514
|
Total output Contigs |
1247
|
1261
|
Total # of singlets |
5072 (58%)
|
5152 (60%)
|
Total # of used EST |
3527 (42%)
|
3362 (40%)
|
Length distribution of EST Sequence of H. erythrogramma
| Minimum | 103 | Mode | 691 |
| Maximum | 801 | Median | 662 |
| Average | 624.5217±123.502 | ||
EST length |
Frequency |
EST length |
Frequency |
EST length |
Frequency |
|---|---|---|---|---|---|
|
< 150
|
81
|
351-400
|
115
|
601-650
|
1568
|
|
151-200
|
98
|
401-450
|
170
|
651-700
|
2889
|
|
201-250
|
100
|
451-500
|
269
|
701-750
|
1795
|
|
251-300
|
87
|
501-550
|
374
|
751-800
|
229
|
|
301-350
|
112
|
551-600
|
711
|
801-850
|
1
|
Length distribution of EST Sequence of H. tuberculata
| Minimum | 102 | Mode | 651 |
| Maximum | 809 | Median | 645 |
| Average | 603.1082±129.1227 | ||
EST length |
Frequency |
EST length |
Frequency |
EST length |
Frequency |
|---|---|---|---|---|---|
|
< 150
|
84
|
351-400
|
187
|
601-650
|
1701
|
|
151-200
|
84
|
401-450
|
202
|
651-700
|
2664
|
|
201-250
|
130
|
451-500
|
345
|
701-750
|
1223
|
|
251-300
|
140
|
501-550
|
542
|
751-800
|
137
|
|
301-350
|
167
|
551-600
|
905
|
801-850
|
3
|
Distribution of No. of ESTs in contigs of H. erythrogramma
| Minimum | 2 | Maximum | 14 |
| Average | 2.8283±1.3696 | ||
Contig length |
Frequency |
Contig length |
Frequency |
Contig length |
Frequency |
|---|---|---|---|---|---|
|
<3
|
999
|
7
|
12
|
11
|
0
|
|
4
|
129
|
8
|
6
|
12
|
0
|
|
5
|
52
|
9
|
7
|
13
|
0
|
|
6
|
37
|
10
|
3
|
14
|
2
|
Distribution of No. of ESTs in contigs of H. tuberculata
| Minimum | 2 | Maximum | 14 |
| Average | 2.6661±1.1759 | ||
Contig length |
Frequency |
Contig length |
Frequency |
Contig length |
Frequency |
|---|---|---|---|---|---|
|
<3
|
1060
|
7
|
11
|
11
|
1
|
|
4
|
119
|
8
|
6
|
12
|
0
|
|
5
|
40
|
9
|
2
|
13
|
0
|
|
6
|
20
|
10
|
1
|
14
|
1
|
Distribution of length of contigs of H. erythrogramma
| Minimum | 214 | Maximum | 2063 |
| Average | 956.1984±317.8372 | ||
Contig length |
Frequency |
Contig length |
Frequency |
|---|---|---|---|
|
<400
|
14
|
1201-1400
|
99
|
|
400-600
|
56
|
1401-1600
|
34
|
|
601-800
|
561
|
1601-1800
|
21
|
|
801-1000
|
241
|
1801-2000
|
4
|
|
1001-1200
|
215
|
2001-2200
|
2
|
Distribution of length of contigs of H. tuberculata
Contig length |
Frequency |
Contig length |
Frequency |
|---|---|---|---|
|
<400
|
12
|
1201-1400
|
92
|
|
400-600
|
88
|
1401-1600
|
36
|
|
601-800
|
515
|
1601-1800
|
5
|
|
801-1000
|
303
|
1801-2000
|
5
|
|
1001-1200
|
204
|
2001-2200
|
1
|
Contributions:
|
Data input into ESTPiper and Perl Scripts:
|
Nathan Nehrt
|
|
Obtaining the Distributions in R:
|
Indrani Sarkar
|
|
Website Page Create and Graph statistic:
|
Chuan-Yih Yu
|
|
Report Writing and Presentation:
|
Sashikiran Challa
|
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