Biotechnology Congress

April 11, 2017, 11:03 pm

≫ Next: Is biotechnology good for carrer

Hi,

As the program manager for upcoming conference 17th Euro Biotechnology congress I would like to bring in to your kind notice regarding conference. The 17th Euro Biotechnology Congress which is going to be held at Berlin, Germany during September 25-27, 2017 will feature speakers from multifarious disciplines. Scientists from all over the world are participating in the meet and will present the latest ground-breaking research in all realms of biotechnology. Focus has been laid on presentations that deal with optimizing industrial processes to increase yield of biotechnology industry and biopharmaceutical products, bio-fuel and bio-energy products. Other than this, research on protein and rDNA technologies including nanotechnology has also been stressed on. I sincerely believe that you will find the conference quite fruitful.
Students interested in attending the international conference in group can avail better discounts on registration.
Best poster and Young research forum is also availed and certification from International organizing committee Members.
For more details follow the link: http://www.biotechnologycongress.com/europe/
Feel free to contact us for more details.

Regards
Kevin Brown
Program Manager
Euro Biotechnology
Conference Series

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Is biotechnology good for carrer

April 16, 2017, 4:55 am

≫ Next: regarding msc in biotechnology

≪ Previous: Biotechnology Congress

Hii sir, i had just given 1st year exam in bsc biotech frm not so famous college...i have lots of doubts as i choosen this field just bcoz i dont want to do eng or such type of degree...i just need a good field to earn money as soon as possible...so can biotech could be better option for me and secondly is college matters for studying any field as to get job?? Also sir my financiall backround is nt so good...so is this field is good for me?? Lastly i want to knw wht is d scope nd exams for msc biotech nd is there any chance in india to have a great job in this feild

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regarding msc in biotechnology

April 17, 2017, 1:10 am

≫ Next: Webinar on Fast and Accurate DNA Variant Calling on 26 Apr 2017

≪ Previous: Is biotechnology good for carrer

hello sir i m persuing my bsc in biotechnology nd now m giving exams of first year from pandit ravishnkr shukla univrsity... will it be effected on my future? as i want to do msc in biotech from req univrsity and i want some bettr job opportunites with expected salary...so plz suggest me wat should i do ? after ug

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Webinar on Fast and Accurate DNA Variant Calling on 26 Apr 2017

April 17, 2017, 4:26 am

≫ Next: Stem cell therapy

≪ Previous: regarding msc in biotechnology

Continuing our DNA-Seq webinar series, we'll present Strand NGS v3.0 best-practices: a workflow that identifies highly accurate variants from raw reads. Our best practices workflow is twice as fast as its GATK counterpart, and results in precision/recall rates of up to 99%/98% on whole exome and whole genome samples. We'll also speak briefly about some of the other features in v3.0 including one-shot pipelines, TSS plots, RNA-Seq performance improvements, and, for the first time, HGVS notations for SNP effect analysis.

Regsiter at http://www.strand-ngs.com/webinar_registration

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Stem cell therapy

April 17, 2017, 5:07 am

≫ Next: Leaving PhD for M.Tech with same Gate Score

≪ Previous: Webinar on Fast and Accurate DNA Variant Calling on 26 Apr 2017

How can we differentiate brain stem cells into any particular type of cell through endogenous stimulation of stem cells? Like if we want to turn brain stem cells into dopaminergic neurons , what could be the therapy for this?

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Leaving PhD for M.Tech with same Gate Score

April 17, 2017, 11:41 pm

≫ Next: I need a help

≪ Previous: Stem cell therapy

Hi Everyone,
I am currently at IISc as PhD candidate(2nd Year). Due to some personal reasons will be leaving the institute by the end of this month. I have applied to few of M.Tech program in IIT's with same gate score(2015) with which I was admitted to IISc. I am concerned on whether my application will be rejected because i have already used gate score(2015) at IISc.

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I need a help

April 18, 2017, 5:53 am

≫ Next: M.tech and PhD after qualifying GATE biotech

≪ Previous: Leaving PhD for M.Tech with same Gate Score

Sir/mam
I am doing my Mtech first year biotechnology programme.I am interested in doing project by using plant source as therapy for treating the provoking disease by protein extraction and purification.But i dont have idea in screening out plant sources and to choose the disease.. Can anyone help me??give suggestions so that i can get through and came out with better idea!! Please

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M.tech and PhD after qualifying GATE biotech

April 19, 2017, 3:37 am

≫ Next: IMPORTANT DOUBTS REGARDING BIOTECHNOLOGY

≪ Previous: I need a help

hello sir,
i have qualified gate 2017 in biotechnology with marks 47.7, score 467 and rank 584 general category. I have a few questions as i am totally confused about what would be best for me.
1- which IITs and NITs can i get ?
2- what is better in NITs? biotechnology or chemical engineering or environmental engineering ?
3- what are the future prospects after doing M.tech from IITs and NITs in terms of placements and pakages?
4- which other colleges take admissions through gate score ?
5- which is a better option after GATE ? PhD or Mtech ?

↧

IMPORTANT DOUBTS REGARDING BIOTECHNOLOGY

April 19, 2017, 6:15 am

≫ Next: Selling of microbes

≪ Previous: M.tech and PhD after qualifying GATE biotech

Hi! I'm a student of HSC 12th from Ruia College Mumbai.. I want to pursue Biotechnology.. But I have a few doubts-
1.Which Institute is the best to pursue Biotechnology in Mumbai after 12th?
2.Is there any entrance exam to prepare for at this point?
3.What is the difference between BSc and B Tech in Biotechnology?
4.Are there any other courses/degrees that can be pursued with biotechnology after 12th?
5.Is there some eligibility criteria to get into a good university after 12th for biotechnology?
6.Is it compulsory to give CET in 12th for admissions in any institute after hsc?

Would be glad if anyone could solve my queries.

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Selling of microbes

April 20, 2017, 6:06 pm

≫ Next: Reqst

≪ Previous: IMPORTANT DOUBTS REGARDING BIOTECHNOLOGY

Guys I have an doubt it is possible or legal to sell micro organism in online and send it through parcel

↧

Reqst

April 22, 2017, 9:01 am

≫ Next: opportunities regarding Msc biotechnology

≪ Previous: Selling of microbes

Hi sir I am doing mtech integrated biotechnology from dy patil biotechnology and uninformative institute pune
This is my first year and m looking for a pharcrutical industry for internship sir plez do help and reply asap

↧

opportunities regarding Msc biotechnology

April 23, 2017, 1:42 am

≫ Next: BINC 2016 Part 1- MCQs

≪ Previous: Reqst

Is there are any extra education needed for such a graduate for working in biotechnology. Industry

↧

BINC 2016 Part 1- MCQs

April 23, 2017, 11:53 pm

≫ Next: BINC 2017 Part 1- MCQs

≪ Previous: opportunities regarding Msc biotechnology

BINC 2016 part 1- MCQs

BioInformatics - 40 questions

1) Which is better - mid-point rooting,outgroup,...
2) How many branches converge at node in tree - 1,2,3,4
3) Rooted tree is given - which taxa are closer to each other
4) Simplest Nucleotide Substitution model - Jukes Cantor,Kimura,....
5) Salt bridges occur between - positive-negative charges,...
6) Why is B-sheet difficult to predict -
7) What is iterated in PSI-BLAST - PSSM,Z-score,E-value,...
8) Which is distance based - Neighbour Joining,Maximum Parsimony,...
9) Causes of overfitting - similar sequences,...
10) Neutral Evolution theory
11) Flux Balance Analysis
12) Flux Balance Analysis
13) Two divergent sequences parallel evolution - Heterosis, Homonomy, Homology, ..
14) Leave-one-out, n-fold theory
15) Coevolution, concerted evolution, Microevolution, ..
16) Artemis - Genome comparison, DNA sequence comparison,...
17) Which is better comparison - Profile vs Profile, Sequence vs Sequence, Profile vs Sequence
18) Bidirectional best hits used in - COG, PDB,....
19) Exon related - it is used
20) Intron related - it is removed
21) H-index used in publications
22) Which step is not there in shotgun sequencing - cloning, sequencing,...
23) PCR related
24) Some scientist used some method to find something - Column chromatography, Electrophoresis,..
25) Chip-seq experiment
26) PFAM made of - profiles, sequences, ...
27) UniGene
28) 7 chain amino acid given - identify by polarity,hydrophobicity, basicity, acidity
29) Non-mutable Amino acid - cysteine,...
30) PAM30, PAM70 some comparison
31) SNP
32) protein homology best shown by - TBLASTX, BLASTP
33) PSSM
34) When to use - BLASTP, TBLASTX, BLASTX
35) 5 questions on E-value, Z-score, P-value - what will happen when one increases, database dependency, similarity, 2 small sequences should be compared by.
till 40

Biology - 20 questions

1) Histones composed of - arginine+lysine, histidine,..
2) Common compound in Glycolysis, Krebbs Cycle.... - Acetyl CoA, pyruvate,...
3) Blood Group Genotypes - 2,3,4,5
4) Pleiotropic gene
5) Where is X seen - Anaphase, prophase, cytokinesis, metaphase
6) Proofreading activity - 5'-3' polymerase activity, 5'-3' exonuclease activity, 3'-5' polymerase activity, 3'-5' ..
7) Phosphofructokinase, polymerase
8) Which is false about Lac operon - negative control, repressor binds to promoter,..
9) Lipid action find false - lipid acts as hormone, all cell membranes contain lipids,..
10) Allosteric Enzyme
11) Allosteric Enzyme

Maths - 5 questions

1) 1 circle inside large circle sharing similar radius-diameter - find shaded area.
2) 2 circles inside large circle - find excluded area
3) probability value can't be negative
4) set theory - 70 people like A, 30 people like B, 10 people like both, total 100 people, how many do not like anything.
5) find wrong notation - sin (inverse) x, sin x(inverse), (sin x) inverse,...

Statistics - 5 questions

1) Binomial Distribution
2) Binomial Distribution
3) Poisson Distribution
4) Poisson Distribution
5) Binomial vs Poisson Distribution

Physics - 5 questions

1) Energy Dimension - MLT,...
2) First Law of Thermodynamics contains - Entropy, Enthalpy, Energy, ..
3) Calculate momentum - values given
4) Carnot engine efficiency, find temperature @ 30% efficiency - values given
5) Enthalpy related

Chemistry - 5 questions

1) Find quantum number for Bohr Radius - values provided
2) Adsorption of hydrogen on platinum - exothermic. endothermic,..
3) Diamond structure - carbon bonds
4) Respiration equation - 1 oxygen molecule gives 1 carbon dioxide
5) Water - specific heat, heat of formation,...

Information Technology - 20 questions

1) kernel, connector, shell
2) line starts with - symbol, root,..
3) grep -v -c
4) grep head -20
5) grep computer$ will find
6) Unix error direction - >>,<<,>,<
7) Not a logical operator - >>,>,=,..
8) Number of operands required in ? operator - 1,2,3,4
9) if statement with logical inputs provided
10) AND operator provides output only when both inputs are true
11) Key value pair in Perl - hash, array,...
12) Not OOP - C,Java,Python,C++
13) Which is the most significant digit in Hexadecimal system
14) DCL statements
15) Class in Java preceded by
16) Operator Overloading example
17) Constructor, Destructor
18)
19)
20)

↧

BINC 2017 Part 1- MCQs

April 24, 2017, 12:03 am

≫ Next: BINC 2017 - Part 2 questions

≪ Previous: BINC 2016 Part 1- MCQs

BIOINFORMATICS - 30 questions

1. STRING does not calculate.
2. Gibbs law representation in mathematical form.
3. Protein-Protein Interactions
4. GEO data set refers to : single set of experiment, single GEO organism,...
5. Zinc is used in X-ray Crystallography for : Phase correction, Stability,...
6. Haemophilia is : X-linked recessive Homolgy trait, Y-linked,...
7. Amino Acid exists in : Neutral & zwitter ionic form, Positive & Negative form,...
8. Silent Mutations caused by : Frameshift, Codon replacement
9. Single continuous diagonal line in dot plot shows : 100% similarity, 80%, 50%, 20%
10. Proteins which do not fold correctly are : discarded, sent back for repair to ribosome, ...
11. In X-ray Crystallography high resolution refers to : lower atomic distance, higher size of crystals, ...
12. AMBER used in : Molecular Dynamic Simulation,...
13. Amino Acids other than 20 are called : Non-Standard, Mutated, Modified Residues,.
14. Homology Modeling is based on : Similarity, ...
15. Phi,Psi for @-helix : 60-40, 60-100, ...
16. RMSD high means : lower similarity in structure, lower similarity in alignment,...
17. Calculate sequence identity by pairwise alignment between 2 given sequences
18. Molecular Dynamic Simulations time used : 2 ns, 10 ns, 2 femtosec, 10 femtosec
19. Masking refers to : LCR,...
20. PDB atom distances given in : ATOM lines, ...
21. NOT a Genome browser : UCSC, DALI, EMBOSS, ...
22. Which is best for aligning sequences : BLAST, PSIBLAST, Needleman-Wunsch,...
23. G-C more stable than A-T because of : 3 hydrogen bonds,...
24. SNP means
25. Primary Structure of protein stabilised by : Covalent, Ionic, Hydrogen bonding, van der Waals.
26. BLOSUM full form
27. Which cause kink in @-helix : Proline, Alanine, ...
28. High G-C content refers to : promoter presence
29. Oligoprotein of single chain : quaternary, tertiary, secondary.
30. Energy depends on : inverse of square of distane between 2 charged particles, inverse of distane , directly proportional,..

Biology - 20 questions

1. RNA editing
2. Restriction Endonuclease
3. Protection of mRNA by : Capping, Tailing,...
4. Vaccine related
5. Intron not present in : Bacteria, Fish, Plant, Fruit fly.
6. Bending DNA domain : double stranded, single stranded,...
7. Semi Conservative Replication means
8. Alternative Splicing done for exons : 75%, 50%, 20%, 100%
9. C-value contains - haploid, diploid,...
10. mitochondrial RNA property
11. Telomeres are present at : middle of chromosome, end of chromosome,...

Physics - 8 questions

1. Gibbs free energy
2. Force is dependent on : inverse of square of distance between 2 particles
3. Potential Energy is dependent on : distance between 2 objects, ...
4. Calculate Force? mass & acceleration given
5. Calculate difference in momentum? velocity difference given
6. Calculate acceleration? speed & distance values provided
7. Calculate acceleration? velocity & time values provided
8. What happens when distance between 2 charged particles is doubled : related to force.

Chemistry - 7 questions

1. Calculate pH of 0.05M HCL
2. Free energy : positive, negative means spontaneous reaction
3. Relation between Boltzman constant, Gas Constant, Avogadro number : R=Nk,...
4. Bent structure of water due to : lone pair of electrons, H-atoms attract each other,...
5. Law of Conservation of Energy : Newton's first law, Second law of thermodynamics,..
6. Entropy of system : closed system, open system,...
7. Enthalpy related

Maths - 8 questions

1. Differentiation
2. Differentiation
3. Matrix (a*b)(b*c) : b[a b c], a[a b c], c[a b c],...
4. Inverse of matrix can be found when : |A| !=0, adj A = 0,...
5. Equation of straight line passing through a point
6. Equation of ellipse passing through 2 points
7. Probability
8. Find maxima of function

Statistics - 7 questions

1. Continuous random variable equation given. Find maxima
2. Find maxima of function
3. Find maxima of function
4. Find maxima of function
5. Poisson distribution
6. Poisson distribution
7. Binomial distribution

Information Technology - 20 questions

1. Which of them always occur together : (Group by,having), (Commit,Rollback),...
2. Operator performs on operand
3. Which OS is time sharing : Linux, DOS,...
4. STAR, BUS, Mesh Topology
5. MongoDB is : NoSQL, RDBMS, DBMS,...
6. who | wc -1 output will be : number of users logged in ,...
7. Piping use
8. grep use
9. Command for renaming : mv, ren, rename,...
10. Encapsulation definition given in question
11. Inheritance example
12. Which is called implicitly when class instance is invoked : Constructor, Destructor,...
13. DML statements : Select Insert Update Delete,...
14. Shell function
15. Kernel function
16. Tuple in DBMS refers to : row in table, column in table,...
17. Which is volatile memory : RAM, ROM, Hard disk, pen drive
18. Geographically separated : MAN,WAN,LAN
19. Operating System Function
20. Scope signifies

↧

BINC 2017 - Part 2 questions

April 24, 2017, 12:29 am

≫ Next: Perl Master Program

≪ Previous: BINC 2017 Part 1- MCQs

PAPER 2 - THEORY

A question paper containing 55 questions (10 pages) is provided. A separate answer sheet (30 pages) to answer 20 questions is given. Each 10 mark answer needs to be written on one side of a page only. Each question is of 10 marks. The marks subdivisions are: 5+5, 6+4, 7+3, 4+3+3, 10.

SECTION - A

Bioinformatics :

1. What is Molecular dynamic simulation. How is temperature increased.

2. Draw Ramachandran plot. Allowed and disallowed regions.

3. Ramachandran plot. Steric hindrance and angles.

4. Amino acids- polar, non-polar, hydrophobic, hydrophilic, aromatic, positive, negative. Why are there some exceptions.

5. QSAR. Pharmacophore model.

6. Docking- rigid flexible semi-flexible. Ligand based drug designing.

7. Monte carlo docking. Structure based drug design.

8. Array express DB. Synonymous SNP vs non synonymous. Role in evolution.

9. Protein threading method.

10. Artificial neural networks. Higher orders (BRNN). Use in secondary structure prediction.

11. Supervised vs unsupervised learning with example.

12. 2d page numerical

13. Fastq format. Something else

14. Flux balance analysis.

15. Rnaseq vs dnaseq.

16. KEGG database. Something else

17. Numerical on dna microarray

18. Numerical on gene expression

19. Denovo assembly

20. Boolean network simulation

21. Leonard jones potential numerical

22. Force field calculation due to torsion angles numerical

23. Gene regulatory networks.

24.

25.

SECTION - B

Biology :

1. Competitive vs non competitive inhibition with diagram and LB plot.

2. Promoter, enhancer, locus region.

3. Operon model. Gene expression

4. Mitochondrial dna related to maternal inheritance.

5. Isozymes. Examples. Something else.

Chemistry:

6. Dissociation constant numerical

7. Bohrs radius numerical

8. Calculate ph.

9. Endergonic vs exergonic reaction. Relation with free energy.

10.

Physics:

11. Fluorescence numerical

12. Enzyme kinetics numerical

13.

14.

15.

SECTION - C

Information Technology :

1. NoSQL merits demerits. GET POST methods in CGI.

2. Pseudocode of adding 2 n*n matrices, the sum of rows and columns of resultant matrix.

3. Program to input 3 words. Calculate vowels and consonants. Toggle upper case lower case. Replace all vowels with x.

4. Program : Result file is provided. 3 columns are : name, roll no, marks. Take marks column. Find the highest and lowest marks. Find average marks.

5. Create table. Perform some operations. Bubble sort algorithm.

Maths :

6. Solve 2nd order linear differential equation.

7. Matrix ‘A’ and inverse matrix given. Find value of : A^2 + 2A + ....

8. Calculate mean and variance of first n natural numbers. Population variance and...

9. Vector numerical.

10. Eigen vector calculation.

Statistics :

11. Binomial distribution numerical

12. Poisson distribution numerical

13. Null hypothesis numerical

14. Markov chain numerical

15. Testing of hypothesis numerical

PAPER 3 - Programming

1a. Intra Molecular Distance Matrix calculation (50 marks) : ATOM lines (155) of a pdb file are provided in input file (only C@ residues). Calculate intra molecular distance between each C@ residue. If distance >= 6, print 1 in distance matrix of output file, else print 0 in distance matrix. Comment on the secondary structures present.

1b. Chou fasman prediction (50 marks) : Amino acid sequence (50 residues) is provided in input file. Extract it. Make octamers of amino acids from the file and calculate their alpha and beta propensity by using second input file. Eg. - 1-8, 2-9, 3-10,....till 50. Second input file contains 20 amino acids with their alpha and beta propensity values in 3 columns. Parse through it using array or store it in a hash. Print the resultant alpha, beta propensity scores for each octamer in output file.

2a. Distance calculation (60 marks) : ATOM lines of a pdb file are provided in input file. Calculate distance between backbone amino acid and side chains. Many other questions were also there.

2b. Gene silencing (40 marks) : mRNA sequence is provided in first input file. miRNA sequences(3) are provided in second input file. Find when gene silencing will occur.

↧

Perl Master Program

April 24, 2017, 12:34 am

≫ Next: Perl Program for Translation

≪ Previous: BINC 2017 - Part 2 questions

#!/usr/bin/perl -w
# Perl programs to find reverse complement, to perform transcription, to convert the DNA to binary form,
# To count the nucleotides, Mutate the DNA, Find the percent identity.
use strict;
my ($file,$line,$dna,$revcom,$rna,$binary,$pos,$newbase,$i,$mutant,$position);
my ($a,$g,$t,$c,$basecount,$nonbase,$percent_ag,$percent_identity,$count) = 0 ;
my @nucs = ('A', 'C', 'G', 'T');

# Ask the user for the fasta filename
print "Enter the fasta filename: ";
$file = <STDIN>;

# Remove the newline from the fasta filename
chomp $file;
# Open the file or exit
open (FILE,$file) or die "Cannot open file : $file \n\n";

# Each line in the file is operated only once by the while loop
# If there are 10 lines in the file then while loop iterates 10 times
# next command tells the while loop to go to the next line
while ($line = <FILE>)
{
# Discard blank lines
if ($line =~ /^\s*$/)
{ next; }

# Discard comment line
elsif ($line=~/^#/)
{ next; }

# Discard fasta header line
elsif ($line=~/^>/)
{ next; }

# Keep concatenating to $dna string
else
{ $dna .= $line; }
}

# Remove whitespaces
$dna =~ s/\s//g;
close FILE;

# Print the extracted nucleotide sequence
print "\nHere is the original DNA : $dna \n\n";

# To find the reverse complement
$revcom = reverse($dna);
# Transliterate operator converts each character individually
$revcom =~ tr/ACGTacgt/TGCAtgca/ ;
print "The reverse complement is : $revcom \n\n";

# To perform transcription
$rna = $dna;
# Substitute operator is used
$rna =~ s/T/U/g;
print "The transcribed RNA is : $rna \n\n";

# To convert the DNA to binary form
$binary = $dna;
#Purine(A,G)--> 1, Pyrimidine(T,C)--> 0
$binary =~ tr/ATGCatgc/10101010/ ;
print "The converted binary format is : $binary \n\n" ;

# To count the nucleotides
$a = ($dna =~ tr/Aa// ) ;
$t = ($dna =~ tr/Tt// ) ;
$g = ($dna =~ tr/Gg// ) ;
$c = ($dna =~ tr/Cc// ) ;
$basecount = ($dna =~ tr/ATGCatgc// ) ;
$nonbase = length ($dna) - $basecount ;
$percent_ag = (($a+$g)/($basecount)*100);
print "Nucleotide Count : \n" ;
print " A=$a \n T=$t \n G=$g \n C=$c \n Total Bases=$basecount \n Errors=$nonbase \n Purine Percentage=$percent_ag \n\n";

# Mutate the DNA 100 times
$mutant = $dna;
for ($i=1 ; $i <= 100 ; $i++)
{
# $pos stores an integer random number between 0 and [(length of $mutant)-1]
$pos = int rand length $mutant;
do
# To select at random one of the four nucleotides.
# [rand @nucs] returns a random integer (0,1,2,3) as there are 4 nucleotides.
{ $newbase = $nucs[rand @nucs];
}
# Make sure it's different from the nucleotide we're mutating. 'ne' stands for not equal to
until ($newbase ne substr($mutant,$pos,1));
# Insert the random nucleotide '$newbase' into the random position '$pos' in the mutant
# In the string '$mutant' at position '$pos' change 1 character to the string in '$newbase'
substr($mutant,$pos,1,$newbase);
}
print "The mutant DNA is : $mutant \n\n";

# Finding the percent identity between input DNA & mutant DNA
for ($position=0; $position < length($mutant) ; $position++)
{
# Match the input DNA with mutant DNA from first position
if(substr($dna,$position,1) eq substr($mutant,$position,1))
{ $count++; }
}
$percent_identity = ($count / (length($mutant)))*100;
print "There are $count identical nucleotides \n";
print "Percent Identity between input DNA & mutant DNA is : $percent_identity \n\n";

↧

Perl Program for Translation

April 24, 2017, 12:38 am

≫ Next: PERL Program - ORF finder

≪ Previous: Perl Master Program

#!/usr/bin/perl -w
use strict;
my ($file,$line,$sequence,$i,$codon,$CODON,$protein);
my %genetic_code = qw(
TTT F
TCT S
TAT Y
TGT C
TTC F
TCC S
TAC Y
TGC C
TTA L
TCA S
TAA _
TGA _
TTG L
TCG S
TAG _
TGG W
CTT L
CCT P
CAT H
CGT R
CTC L
CCC P
CAC H
CGC R
CTA L
CCA P
CAA Q
CGA R
CTG L
CCG P
CAG Q
CGG R
ATT I
ACT T
AAT N
AGT S
ATC I
ACC T
AAC N
AGC S
ATA I
ACA T
AAA K
AGA R
ATG M
ACG T
AAG K
AGG R
GTT V
GCT A
GAT D
GGT G
GTC V
GCC A
GAC D
GGC G
GTA V
GCA A
GAA E
GGA G
GTG V
GCG A
GAG E
GGG G
);

print "Enter the filename: ";
$file = <STDIN>;
chomp $file;
open (FILE, $file) or die "Cannot open file : $file \n\n";
# if there are 10 lines in the file then while loop iterates 10 times
# next command resets the while loop to the next line
while ($line = <FILE>)
{
# Discard blank lines
if ($line =~ /^\s*#/ )
{ next; }
# Discard comment line
elsif ($line=~/^#/)
{ next; }
# Discard fasta header line
elsif($line =~ /^>/ )
{ next; }
# Keep concatenating to $sequence string
else
{ $sequence .= $line; }
}
$sequence =~ s/\s//g ;
close FILE;

for ($i=0; $i < (length ($sequence) - 2) ; $i += 3)
{
# From the string '$sequence' at position '$i' extract 3 characters & store it in '$codon'
$codon = (substr($sequence,$i,3));
# Converting any lower case characters to upper case
$CODON = uc $codon;
# Checking for the existence of CODON in the hash %genetic_code
if(exists $genetic_code{$CODON})
# The corresponding amino acid in the hash is stored in $protein
{ $protein .= $genetic_code{$CODON}; }
else
{ die "Bad codon !! \n\n";}
}

print "The translated protein sequence is : $protein \n\n";

↧

PERL Program - ORF finder

April 24, 2017, 12:46 am

≫ Next: PERL Program - Matrix Transpose

≪ Previous: Perl Program for Translation

#!/usr/bin/perl -w
use strict;
my ($file,$line,$dna,$revcom,$i,$codon,@frames_array,$j,$orf);
my ($frame1,$frame2,$frame3,$frame4,$frame5,$frame6)='';

print "Enter the filename: ";
$file = <STDIN>;
chomp $file;
open (FILE, $file) or
die "Cannot open file : $file \n\n";
while ($line = <FILE>)
{
if ($line =~ /^#/ )
{ next; }
elsif($line =~ /^>/ )
{ next; }
else
{ $dna .= $line; }
}
$dna =~ s/\s//g ;
close FILE;

print "Original Sequence is: $dna \n";

# Assigning 3 frames for the forward strand
for ($i=0; $i<length($dna)-2; $i+=3)
{
$codon = substr($dna,$i,3);
$frame1 .=$codon;
}

for ($i=1; $i<length($dna)-2; $i+=3)
{
$codon = substr($dna,$i,3);
$frame2 .=$codon;
}

for ($i=2; $i<length($dna)-2; $i+=3)
{
$codon = substr($dna,$i,3);
$frame3 .=$codon;
}

# Assigning 3 frames for the reverse complementary strand
$revcom = reverse($dna);
$revcom =~ tr/AaTtGgCc/TtAaCcGg/;

for ($i=0; $i<length($revcom)-2; $i+=3)
{
$codon = substr($revcom,$i,3);
$frame4 .=$codon;
}

for ($i=1; $i<length($revcom)-2; $i+=3)
{
$codon = substr($revcom,$i,3);
$frame5 .=$codon;
}

for ($i=2; $i<length($revcom)-2; $i+=3)
{
$codon = substr($revcom,$i,3);
$frame6 .=$codon;
}

print "Frame1: $frame1 \nFrame2: $frame2 \nFrame3: $frame3 \nFrame4: $frame4 \nFrame5: $frame5 \nFrame6: $frame6 \n" ;
@frames_array=($frame1,$frame2,$frame3,$frame4,$frame5,$frame6);
# Perl assigns the first element of the array at 0th position
for($i=0; $i<6; $i++)
{
# Match ATG-> START codon, then match at least 50 nucleotides, then match either of (TAA|TAG|TGA)-> STOP codons,
# g-> globally, i-> case insensitive. This match finds the first ATG and the last STOP codon in the frame.
if ($frames_array[$i] =~ m/(ATG)(.{50,})(TAA|TAG|TGA)/gi)
{
# $1 stands for (ATG), $2 stands for (.{50,}), $3 stands for (TAA|TAG|TGA)
$orf = $1.$2.$3;
$j = $i+1;
print "\n ORF found at Frame$j : $orf \n";
}
}

↧

PERL Program - Matrix Transpose

April 24, 2017, 10:04 pm

≫ Next: PERL Program - Matrix Addition

≪ Previous: PERL Program - ORF finder

print "Enter 3*3 Array Elements : ";
for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
$matrix[$row][$col] = <STDIN>;
}
}

# Print the original matrix
print "Entered Matrix is : \n";
for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
printf("%3d", $matrix[$row][$col]);
}
print "\n";
}

#Transposing the matrix
for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
$matrix_transpose[$row][$col] = $matrix[$col][$row];
}
}

# Print the matrix in 3 integer spaces : "%3d"
print "Transpose of the Matrix is :\n";
for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
printf("%3d", $matrix_transpose[$row][$col]);
}
print "\n";
}

# Check for Symmetric Matrix
$isSymmetric = 0;
for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
if ($matrix[$row][$col] != $matrix[$col][$row])
{ $isSymmetric = 1; print $isSymmetric; }
}
}
if($isSymmetric==0)
{ print("Matrix is symmetric. \n"); }
else
{ print("Matrix is not symmetric. \n"); }

↧

PERL Program - Matrix Addition

April 24, 2017, 10:05 pm

≫ Next: PERL Program - BINC 2015 question

≪ Previous: PERL Program - Matrix Transpose

print "Enter elements in matrix A of size 3x3: \n";
for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
$A[$row][$col] = <STDIN>;
}
}

print "Enter elements in matrix B of size 3x3: \n";
for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
$B[$row][$col] = <STDIN>;
}
}

for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
$C[$row][$col] = $A[$row][$col] + $B[$row][$col] ;
}
}

print "Sum of the Matrices A+B is : \n";
for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
printf("%3d", $C[$row][$col]);
}
print "\n";
}

↧

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