...a brief introduction
about myself
Gopa kumar G
Aswathy, Uppoodu, East Kallada(P.O)
Kollam, Kerala,India-691502
ph:+91 0474 2585037
email:-gopakumar.cbi@gmail.com, gopakumarg78@rediffmail.com
Academic
Profile:-
- MPhil Bioinformatics, at Centre for Bioinformatics,
University of Kerala, result awaiting.
- MTech in Software Engineering, from Cochin University
of Science and technology, securing First
Rank, 82.6%
- BTech in Computer Engineering, from Cochin University
of Science and technology, securing First
class with Distiction, 82.01%
Professional
Experience:-
- Worked as Lecturer in Computer Science and Engineering,
College of Engineering Perumon, Kollam for a period
of one and half years.
- Worked as Lecturer in Computer Science and Engineering,
College of Engineering Trikaripur, Kasargod for
a period of eight months.
-
Worked as lecturer in Computer Science and Engineering (contract
basis), University College of Engineering, Kariavattom,Thiruvananthapuram
for a period of four months.
Other
Achievements:-
My
Favourite Subjects:-
- Academic:- Bioinformatics (especially
gene finding & protein folding), Automata Theory,
Networking (computer and cellular), C, Compiler Design
- Non Academic:- Science Fiction
Dowonloads:-
Future
plans:-
- To study Sanskrit and Vedas
Interesting
Place to Visit:-
- The place beyond my eyesight.
Most
influenced persons:-
- Srinivasa Ramanujan (particularly his famous number
1729), all my teachers especially Kallada V V Kutty Sir,
Sura Sir, Jayakumar Sir and Achu Sir, my mother and
father. Last, but not the least, my brainchild, my divine
guidance, my greatest inspiration...whose presence is
always with me through my senses.
Leisure
time spent by:-
- Listening to Music (especially malayalam classical
melodies)
- Day dreaming
- Reading scientific articles
- Playing chess, badminton etc
A
Simple Question To Answer:-
Are you a person with Biology/Biochemistry/Bioinformatics/Biotechnology
background?... if so, try to answer the question after reading
the following paragraph.....Click here
My Small Articles:-
What
a SIMILARITY!!!
-
Prokaryotic
protein synthesis is similar to INTERPRETATION
of programming languages - mRNA to protein conversion
taking place in the same place. That is in the same platform.
Similar to PERL language.
-
Eukaryotic
protein sysnthesis is similar to COMPILED and
INTERPRETED behaviour of programming languages.
That is mRNA is produced inside the nucleus and protein
is sysnthesised in the cytoplasm. They are different platforms/environments.
It is like JAVA programming language. ( Whether a complete
platform independence is there? that is mRNA produced
in one tissue/cell is being taken to another tissue/cell
and making proteins there???)
Back
Newly
coined terms
- CAN:-
Cellular Area
Networks,
which represents the network of all the cells inside a living
organism. This can be considered like the Internet. Internet
connects different types of computer networks. Similarly
CAN also connects different types of cellular networks in
a living body.
Back
BIOWITS from
the magical helix
1: The only animal present inside all the DNA is?
2: It is used for tying the DNA?
3: The weapon present inside the DNA is?
4: Name the certificate which can be obtained from DNA?
5: Name of the international treaty present inside the DNA
is?
6: What you will get, if you reverse DNA?
7: Name the mobile service present inside all the living organisms?
8: Name the hot beverage present inside the DNA molecule?
9: Which multinational company got its name from the DNA molecule?
10: Name the middle letter in DNA?
11: Film stars' must have this DNA part?
12: Can you name the place where sea and tea lie side-by-side?
Latest (updated on 04/06/2005)
13:You can see this animal if you identify 2 new special
amino acids?
14 :Most life on this earth starts with this letter!!!
15 :‘I’ am present but ‘you’
are not. Can you say where this happens.
16 :You can make this very easily if you identify the 3 new
amino acids X, O & B
17 : You will surely get this, if you identify the 3 new amino
acids O, J & B
Answers: 1)CAT 2) TAG 3)GAT 4)TC (Transfer Certificate)
5) GATT 6)AND 7) CellOne 8) T 9)TATA 10) N 11) ACT 12) in
the DNA(CT) 13) OX 14) M
15) in proteins (U is absent) 16) BOX 17) JOB
Back
BIOINFORMATICS- expanded
Each word points to the unique features of BIOINFORMATICS.
If you read from top to bottom, take the groups of words where
dots are put, you can find out the definition, real aim and
power of this new emerging interdisciplinary scientific field.
B iology
I ntegrated
O nline
I nformation
Technology...........
N ovel
F indings
O n
R emedies.......................
M athematically
A nalyzed
T heoritically
I lluminated
C oncrete
S olution
...........................
Back
THE PEPTIDE CHAIN SIGNIFICANCE-You
carefully read the following paragraph and try to identify
the speciality present....
My
cells’ centers maintain the ascendance in achieving all the
physical activities related with me. Many peptide chains aggregate
in attaining a cell’s tasks. These peptide chains are created
in series steps. The chemical catalysts present in cells,
imitate the gene, DNA part, present in the genetic data. This
gives the messenger RNA (mRNA). Then the mRNA is translated
inside the peptide making machinery. A cell has many peptide
chain making machineries. All these machineries helps in making
a cell’s needed peptide chains. All these peptide chains aggregate
in realising cells’ activities, which preserve all the Earth’s
living things.
............got it? if not click here.
Back
THE STORY BEHIND THE
STORY
Prajanan
was the king of Prapyam. He had only one daughter named Priyamvada.
He loved his daughter very much. Priyamvada was a charming,
young and dynamic girl. She was very honest also.
One
day she went for a picnic in the forest with her maid. On
the way she saw an old man lying. She stopped her journey
and went near to him. The old man was suffering from fever
and he was not even able to sit. She gave him food, water
and treated him with great respect.The old man felt great
relief,he blessed Priyamvada and presented her a magic ribbon
named "KENDRAAMLAM". He enchanted her a set
of “mantras” also. He then described to her the magical properties
of the ribbon. According to him, the ribbon can produce a
variety of things by simply enchanting the mantras while holding
the ribbon at various positions. Atlast he warned her that
do not hold the ribbon at particular positions while enhanting
some mantras. He blessed her and Priyamva continued her journey.
On
the way she decided to test the magical effect of the ribbon.
She enchanted the mantra "VIVIDHA" and was
surprised by seeing the various beautiful things she got from
the ribbon. She came back to her palace.She told all the story
to her parents.They were also very much surprised by hearing
the story. One day she entered a hot room in the palace and
enchanted a mantra named "ANATHAAMLAYAH", while
holding the ribbon. She got surprised by seeing a numerous
ribbons.She couldn’t believe her eyes.
After
some days, she was recollecting some special mantras enchanted
by the old man. While uttering a special mantra called "KHADGAYA",
the ribbon in her hands was cut into two pieces. She cried
a lot and prayed in deep agony.Atlast, she decided to utter
all the mantras she knew. While uttering a mantra named "EAKATHA",
the two ribbon parts joined together to form the original
one.
Years went like days. One day Priyamvada decided to check
whether the dangerous positions of the ribbon will work or
not. For a moment she ignored the old man’s advice. She started
enchanting a mantra named "ANTHYAH". While
enchanting that mantra,her body began to swet.Her hands were
shivering ,she became unconscious and fell down. That was
her last breath.....!!!
THE REAL ACTORS
"KENDRAAMLAM" -DNA
"VIVIDHA" - Proteins,tRNA,rRNA
positions of ribbon-gene locations.
hot room - PCR environment
"ANATHAAMLAYAH" - PCR Mantra
ribbon cut into pieces-restriction endonuclease
"KHADGAYA"- Restriction mantra
parts of ribbon joined together-ligase enzyme.
"EAKATHA"- Joining mantra.
dangerous part of ribbon-junk DNA? or introns?
regulatory regions?
"ANTHYAH" - Danger Mantra
Prajanan- A Parent Cell
Priyamvada - A Daughter Cell
Prapyam - A Tissue or an Organ
old man - ?????
Back
A
Context-Free Grammar (CFG) for creating sentences in the "LANGUAGE OF LIFE"
1. <protein>--><polypeptide chain>
2. <polypeptide
chain>--><amino acid residues>
3. <amino
acid residues>--><amino acid><amino
acid residues>|<amino acid><amino acid>
4. <amino
acid>--><A>|<C>|<D>|<E>|<F>|<G>|<H>|<I>|<K>|
<L>|<M>|<N>|<P>|<Q>|<R>|<S>|<T>|<V>|<W>|<Y>
5.<A>|<C>|<D>|<E>|<F>|<G>|<H>|<I>|<K>|<L>|<M>|<N>|<P>|<Q><R>|
<S>| <T>|<V>| <W>|<Y>--><codon>
6. <codon>--><nucleotide><nucleotide><nucleotide>
7. <nucleotide>
-->a|g|c|t
The above CFG gives the rules (productions) for creating
sentences in the LANGUAGE OF LIFE…….The
terms inside the angle brackets are variables and those with
out angle brackets are terminals. In this case, protein, polypeptide
chain, amino acid residues, amino acid, A, C,…,Y, codon and
nucleotide are variables while a, g, c, t are terminals.
The possible codons for each amino acid are given below:-
<A> -->gca|gcc|gcg|gct
<C>-->tgc|tgt
<D>--> gac|gat
<E>--> gaa|gag
<F>-->ttc|ttt
<G>--> gga|ggc|ggg|ggt
<H>--> cac|cat
<I>--> ata|atc|att
<K>-->aaa|aag
<L>--> tta|ttg|cta|ctc|ctg|ctt
<M>--> atg
<N>--> aac|aat
<P>--> cca|ccc|ccg|cct
<Q>--> caa|cag
<R>--> cga|cgc|cgg|cgt|aga|agg
<S>--> tca|tcc|tcg|tct|agt|agc
<T>--> aca|acc|acg|act
<V>--> gta|gtc|gtg|gtt
<W>--> tgg
<Y>--> tac|tat
For common usage, the rule (production) numbered ‘2'
can be changed to:
<polypeptide chain>--><M><amino acid
residues>
because most of the proteins begins with the amino acid Methionine.
With the use of above CFG we can easily create all
the sentences in the LANGUAGE OF LIFE...!!!
Back
Answer
to the Question…WHETHER THE ABOVE PARAGRAPH
IS A PROTEIN SEQUENCE!!!MAY BE!!! REMOVE ALL THE SPACES, PUNCTUATION
SYMBOLS, and BRACKETS etc…… !!!YOU WILL GET A PROBABLE PROTEIN
SEQUENCE !!! The words in the paragraph contain only the 20
letters of amino acids...devoid of letters B,J,O,U,X &
Z....!!!
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