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Genomics and Applied Biology 2014, Vol. 5, No. 5, 1-6
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2.2 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 finally 6999
contigs generated with average value of 302 by this
software and other details are shown in Table 2.
Table 2 Contig measurement
Description
Length
N75
248
N50
293
N25
374
Minimum
187
Maximum
5386
Average
302
Count (Contigs)
6999
2.3 Functional annotation with BLASTX and
blast2GO
2.3.1 BLASTX
BLASTX was performed to align the contigs against
non-redundant sequences database using an E value
threshold of 10-6. Out of 6999 transcript contigs, 1988
were having BLAST hits to known proteins with high
significant similarity and 102 had no BLAST hits
(Table 3). Out of total transcripts contigs, Table 4 and
Figure 1 shows that species distribution in which 2378
sequences showed significant similarity with
Phaseolus
vulgaris
itself and least similarity was found with
Nicotiana tabacum
(5).
2.3.2 Enzyme Code (EC) Classification
Enzyme classified with total of 563 sequences
which is further classified into six classes which are of
Table 3 Blast Result
Without Blast Results
102
Without Blast Hits
2601
With Blast Results
1988
With Mapping Results
629
Annotated Sequences
1679
Total Sequences
6999
Table 4 Blast Result of Species Distribution
Species
Blast Hit
Phaseolus vulgaris
2378
Glycine max
274
Medicago truncatula
149
Vitis vinifera
141
Eucalyptus grandis
90
Cicer arietinum
81
Citrus sinensis
79
Populus trichocarpa
76
Arabidopsis thaliana
70
Morus notabilis
62
Theobroma cacao
60
Fragaria vesca
59
Ricinus communis
58
Cucumis sativus
54
Prunus persica
52
Solanum tuberosum
48
Arabidopsis lyrata
45
Prunus mume
45
Jatropha curcas
44
Erythranthe guttata
43
Citrus clementina
39
Capsella rubella
39
Eutrema salsugineum
38
Solanum lycopersicum
36
Genlisea aurea
34
Lotus japonicus
25
Millettia pinnata
10
Vicia faba
6
Nicotiana tabacum
5
others
156
Figure 1 Blast Result of Species Distribution