Blast

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Christian Jirard Z. Custodio
1. blastn of the rice nucleotide sequence
The data presented by BLAST for the given rice nucleotide sequence predicts
the probable identity of the gene in the query. A graphic summary illustrates the
distribution of the 122 Blast Hits on the query sequence, and based on the color key
assigned for alignment scores, all hits scored greater than or equal to 200 except for
one segment. The succeeding table describes further the sequences which produced
significant alignments by providing statistical data. Again, given the top three sequences
shown, their max scores, which is 1615, are equal to the total scores calculated except
with the third sequence giving an even higher score. Also, as illustrated in the graphical
summary, their query covers are 100%. Moreover, their percent identities were all 99%.
These data supports that the hits had a strong alignment with the query. Lastly,
considering the E values that are zero, meaning that there is zero per cent chance that
the alignments were a result of chance, the most probable identity of the query
sequence is Oryza sativa Japonica Group oxalate oxidase gene.
2. blastp of the rice amino acid sequence
The data presented by BLAST for the given rice amino acid sequence predicts
the probable identity of the protein in the query. Considering the hits that gave 99% per
cent identity and the lowest E value, the most probable identity is oxalate oxidase of the
Oryza sativa Japonica Group. The software also presented a more specific probable
identity which is Cupin_1 of the ABD superfamily. However, since the top scoring and
highest per cent identity sequence had an E value of 1e-160, it is slightly possible that
the alignment was obtained only by chance.
3. pairwise alignment of sequence x and sequence y
Alignment of sequence x and sequence y by BLAST showed 90% identity. This
means that sequence x is highly similar to sequence y. Having an E-value of 0.0, there
is no possibility that the obtained alignment was a result of chance. The succeeding
illustration shows the location of gaps in the alignment. These gaps are also apparent in
the dot matrix graph present. Moreover from the presented data, sequence y covered
only 74% of sequence x, meaning that sequence y may only be a part of sequence x.
Also, as shown by the dot matrix graph and the alignment illustration, a short sequence
from the minus strand of sequence y aligns with the positive strand of sequence x
having 79% identity. In addition, with an expect value of 0.030, there is a probability that
the alignment was only a result of chance.

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