November 15, 2017 Wednesday
Bedtime Story
Heuristics in BLAST
Last night I had introduced you to the
BLAST or the Basic Local Alignment Search Tool that is used for comparing
primary biological sequence information.
Note the last word of the sentence –
information!
That is what principally the biological
organic molecules store to create meaning out of nothing.
The beauty of this program is that is
anywhere in this small world the code of any gene is discovered and published,
one can use this information to find that if that specific gene is present in
the known genome of any other species including that of human ape.
Like everything in the universe, BLAST too
has an evolutionary history.
BLAST was not the first algorithm as before
it there came FASTA (stands for FAST-All) in 1985 and before that there existed
Smith-Waterman algorithm.
I will not go into the details of these
algorithms but there is one thing that I must say.
Smith-Waterman algorithm differs in one
very fundamental way from FASTA and BLAST in that the later two algorithms use
largely heuristic method to carry out the execution.
Our human brain too largely uses heuristic
technique for its problem solving, learning and discovery.
Heuristics are mental or rather
computational short cuts (since now even machines use them) that dramatically
decrease the cognitive load in decision making.
Some examples of heuristics in human mental
computing include stereotyping, profiling, common-sense, rule of thumb,
educated guess and intuitive judgment.
As you can very well understand without
having me to point out, all these cognitive mode of thought process often lead
to serious errors.
An elementary example would be that any
Arab from Afghanistan would be mentally pictured to be a terrorist by most
American apes.
Similarly all black Africans are considered
by most Indian apes as good-for-nothing, high-on-testosterone drug peddlers.
Yet, in spite of all its flaws,
evolutionarily heuristic computing and cognition has proven to be overall a
very successful strategy.
Analogously when it comes to algorithms for
matching amino acid or nucleotide sequence, both BLAST and FASTA greatly
enhance the speed of matching in most cases, though “it cannot guarantee the
optimal alignments of the query and data base sequences” as Smith-Waterman
algorithm does.
On the other hand the precision and high
accuracy of Smith-Waterman algorithm comes at the expense of time and computing
power.
Despite the inherent weaknesses in accuracy
of the BLAST algorithm, Mojica struck gold when he used it for analyzing the
spacer sequences spacer parts of the repeat-spacer array of CRISPR genes.
Stay tuned to the voice of an average story storytelling
chimpanzee or login at http://panarrans.blogspot.com
Good night mon ami and my fellow cousin ape.
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Another great educator and a teacher that I am aware of is
Professor Subhashish Chattopadhyay in Bangalore, India.
While I narrate stories, Professor Subhashish an electronic
engineer and a former professor at BARC, does and teaches real mathematics and
physics.
He started the participation of Indian students at the
International Physics Olympiad.
Do visit him here:
All his books can be downloaded for free through this link:
For edutainment and English education of your children, I
recommend this large collection of Halloween Songs for Kids:
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