基本HTML版本
Computational Molecular Biology 2014, Vol. 4, No. 9, 1-6
http://cmb.biopublisher.ca
3
Table 1 Species comparison based on sequence
Species
SRR Number
Reads
%GC Content
Platform
Arachis hypogaea
L.
SRR1212866
7.3 M spots
48.5
Illumina HiSeq 2000
Cicer arietinum
L.
SRR627764
36 M spots
41.8
Illumina
Phaseolus vulgaris
L.
SRR1283084
20.4 M spots
46.4
Illumina HiSeq 2000
Trigonella foenum-graecum
L.
SRR066197
627,117 spots
45.2
454 GS FLX
Vicia sativa
L.
SRR403901
12.4 M spots
42.4
Illumina HiSeq 2000
Table 2 NGS QC Toolkit Result
Species
Total number of
reads (Original
File)
Total number of reads
(High Quality (HQ)
Filter file)
Total number of
bases (Original
File)
Total number of
bases (High Quality
(HQ) Filter file)
Percentage of
HQ reads
Arachis hypogaea
L.
7300624
7216150
365031200
360807500
98.84%
Cicer arietinum
L.
1942297463
1942030133
1904983
1904959
99.99%
Phaseolus vulgaris
L.
20444892
13418027
1042689492
684319377
65.63%
Trigonella foenum-graecum
L.
627117
609237
146335656
141577237
97.15%
Vicia sativa
L.
12427455
12131939
608945295
594465011
97.62%
2.3 De novo Sequence Assembly
CLC GENOMICS WORKBENCH 7 considered for
de novo sequence assembly with by default parameters
like Mismatch Cost = 2, Insertion Cost = 3, Deletion
Cost = 3, Length Fraction = 0.5, Similarity Fraction =
0.8, Word size = 21 and contigs generated with
average values by this software and other details are
shown in Table 3.
Table 3 Contig measurement in Length
Species
N50
Minimum
Maximum
Average
Count (Contigs)
Arachis hypogaea
L.
448
199
6635
425
10824
Cicer arietinum
L.
1239
179
8439
805
34678
Phaseolus vulgaris
L.
293
187
5386
302
6999
Trigonella foenum-graecum
L.
470
86
3231
445
7256
Vicia sativa
L.
588
197
6080
503
22748
2.4 Functional annotation with BLASTX and blast2GO
2.4.1 BLASTX
BLASTX was performed to align the contigs against
non-redundant sequences database using an E value
threshold of 10-6. Various statistical information of
BLAST result is given in Table 4.
2.4.2 Enzyme Code (EC) Classification
Enzyme classified with sequences which are further
classified into six classes which are of
Oxidoreductases, Transferases, Hydrolases, Lyases,
Isomerases and Ligases which is shown in Table 5.
Table 4 Blast Result comparison
Species
Without Blast
Results
Without Blast
Hits
With Blast
Results
With Mapping
Results
Annotated
Sequences
Total Sequences
Arachis hypogaea
L.
60
688
4789
568
4719
10824
Cicer arietinum
L.
3492
3996
25459
786
945
34678
Phaseolus vulgaris
L.
102
2601
1988
629
1679
6999
Trigonella foenum-graecum
L.
167
2656
1983
192
2258
7256
Vicia sativa
L.
0
1114
13482
500
7652
22748