Biotechnology Forums - Bioinformatics

Gene specific marker development

Thu, 30 Jan 2020 07:45:52 +0000

Hello everyone

I am working on Whole Genome BSA re-sequencing.. and found variations between resistant and susceptible bulks and narrowed down to variation in 30 kb region on one chromosome. Now I want to develop overlapping primers for the specific region.. Can anyone please describe me the procedure for developing the same ....

Thank you

Any user friendly way to find rare mutations in whole genome raw?

Tue, 07 Jan 2020 22:54:39 +0000

Is there any user friendly way to find rare mutations in the individual human whole genome sequencing raw data? (from Dante, 30x coverage).

To be more specific, I want to find mutations from this paper: https://docs.google.com/document/d/1EkRM...sp=sharing (it's very short, less than one page).

But I'm confused. In their paper they just talk about genes (RAD21, B3GAT2, SMC3, SCN11A , SCN5A, SCN9A, SCN10A, SCN11A, TRPA1), but not mutations? Can we find thats diseased-mutations which they talking about in genes, which their list? Or is there not enough data in the paper/study for this?

And if there is not enough data, which data I need to request from authors?

Or those genes have kind a "gold standard sequences" and if that sequence different from standard - there is "diseased" gene? (I have only very basic genetics and bioinformatics knowledges)

Perl programming

Tue, 23 Oct 2018 18:30:51 +0000

Hello
From where i can learn perl programming for bioinformatics??

Books

Mon, 13 Aug 2018 17:23:05 +0000

Can anyone send me the soft copy of "Bioinformatics- Methods and Applications: Genomics, Proteomics and Drug Discovery"(4th edition) by S.C. Rastogi, P. Rastogi, N. Mendiratta

Dissertation Related query

Mon, 30 Jul 2018 16:18:12 +0000

I am pursuing M.Sc in Biotechnology. What project should I choose for my M.Sc dissertation? Specially i m interested for Bioinformatics. So please suggest me some bioinformatics related topics for my dissertation. Thank u

BINC 2018 Part 1- MCQs

Sun, 01 Jul 2018 07:08:20 +0000

BIOINFORMATICS - 40 questions

1. Which is not part of Gene Ontology : Cellular function, Molecular Function, Biological process, Cellular localisation.
2. If 1 base pair=1 bit, what will be the size of human genome : 3 GB, 30 GB,....
3. Homology based question on 3 sequences using BLAST.
4. MUMmer related..
5. PAM is based on : closely related protein sequences,...
6. PSI BLAST sensitivity can be increased by : decreasing the E-value cutoff, reducing the number of iterations...
7. Progressive multiple alignment done by...
8. UniRef DB : filters data based on some threshold...
9. E-value depends on : size of query and database size,...
10. Important steps in docking : simulation and scoring,...
11. Gold,Autodock use : stochastic learning, machine learning,...
12. MEME best used for finding motifs : ungapped & variable length, gapped & fixed length, ungapped & fixed length,...
13. Neighbour Joining calculation is more complex than UPGMA method.
14. Phylogram given : find which are more related to each other..
15. Van der Waals force : due to transient dipoles,....
16. Hydrogen bond : cumulative effect is strong, stronger than electrostatic bond,...
17. STRING is not based on : literature mining, protein interactions,...
18. Molecular Dynamic Simulations energy given -2000 kcal\mol...
19. What is the initial condition for MDS : equilibrium, energy,....
20. A+G=T+C, A+T=G+C, A\T=G\C, A\G=T\C.
21. PubMED extracts information based on MeSH terms.
22. Levinthal paradox : protein takes infinite time to fold,...
23. Which BLOSUM to use for highly divergent sequences : BLOSUM : 45,60,70,90
24. Ramachandran plot allowed regions fall in which quadrant : 4, 2&3, 1, 1&4.
25. Ramachandran paper about some triple helix structure...
26. A 100 amino acid chain contains 3, 20 polar amino acid group separated by 7-10 non polar amino acid : it will be alpha helix, beta strand, transmembrane
27. DSSP structure given : classify as : alpha\beta, alpha+beta, alpha, beta
28. Protein structure classified using : SCOP, CATH, FSSP, DALI.
29. Protein-dna interaction occurs by : major groove interacts with protein, phosphate bond,...
30. Entropy of 3 peptides increasing order : Val+Ala+Gly+Ala+Pro, Phe+Met+Ser+Ala+Val, Leu+Lys+Ser+Cys+Trp
31. PubChem does not contain this column : InChi, canonical SMILES, DrugBankId, IUPAC.
32. Prosite regular expression usage of {} and []
33. Regular expression AA[CD]S{F} meaning: find correct option...
34. Multi dimension substitution matrix disadvantages...
35. Concentration of receptor-ligand should be high for strong interaction.
36.
37.
38.
39.
40.

Biology - 20 questions

1. Lac operon related.
2. ABO blood system represents..
3. Codominance related
4. Codominance related
5. Stability of DNA increases on adding : HCL,phenol,ethanol,alcohol.
6. Enantiomer related
7. Drone bee worker contains genetic material from : mother,mother+father,father,worker
8. Post translational modification binding site.
9. MicroRNA related.
10. Pea plant experiment
11. Southern blotting, Western blotting, northern blotting use
12. Prokaryotic gene expression
13. Codon bias refers to
14. Turners syndrome
15. Glycosidic linkage
16. Alpha beta promoter in some organism
17. Paralogs obtained by gene duplication
18. Collagen structure : triple helix stabilised by
19. arrange 3 peptides according to length: beta hairpin, alpha helix, 3-10 helix, beta strand
20.

Physics - 5 questions

1. Find wavelength of electron : mass and charge of electron given, Plancks constant given, velocity=3*10^7 m\s.... 2.4 Angstrom,0.24 Angstrom,24 Angstrom
2. Velocity acceleration time equation in other form..
3. Potential Energy calculation for moving a unit mass of charge from 2 meter to 5 meter in presence of another charge...
4. Height to which a man can jump on Mars which has half radius of earth & one-tenth the mass of earth..1.7m, 2.4m, 5m.
5. Energy is inversely related to distance by : sixth power, square root, square, cube.

Chemistry - 5 questions

1. What will happen to pOH of a solution: when pH increases,..
2. Hybridisation states for : No2+, NO3-, NH4+ : (sp,sp2,sp3), (sp2,sp,sp3),...
3. Entropy increases in which order for 3 compounds : CH3-CH2-CH2-CH2-CH2-CH3, CH3-CH2-CH-CH-CH2-CH3, CH3-CH-CH-CH-CH-CH3...
4. Work done for 1 degree rise in temperature when pressure remains constant..
5. Lineweaver-Burke plot false statement..

Maths - 5 questions

1. Find limit of..
2. Probability when 3 coins tossed...output is even numbers and odd number...
3. Find the value of : 1^2 - 2^2 + 3^2 - 4^2 + ..... + 99^2 - 100^2 ? -5050, -13050,...
4. Equation of parabola passing through 2 points tangent to a circle..
5. In which quadrant will e^x lie for all real x : 1&3, only 2, only 3...

Statistics - 5 questions

1. Binomial Distribution
2. Find mean and variance for single continuous variable..
3. Find mean and variance of..
4. Find conditional probability..
5. Independent event occurs when : P(A U B)=0, P(A\B)=P(B\A)...

Information Technology - 20 questions

1. Perl code: array contains 4 elements...what is $array[2]?...answer will be the 3rd element.
2. In C program : what will "ls file.txt" print?
3. In Unix : "ln -l" : will create soft link or hard link?
4. IDE fullform : Integrated Development Environment.
5. In Unix : Kernel is at the core.
6. Which command not present in SQL : Choose,Drop,Select,Update.
7. Find correct syntax of : Switch case, For loop, if condition, do while.
8. Operating System related
9. Command for listing contents..
10. Do while loop will : work atleast once, execute1 time less than condition, execute 1 time more than condition
11. File sequence contains : linear files...
12. Cluster computing allots dynamic memory to each system..
13. Parallel computing scaling done by..
14. Logical record in DB refers to : complete information of a single line
15. Parallel computing related..
16. Unix feature related..
17. Application Programming Interface related..
18. getch() command in which header file ? conio.h, stdio.h, io.h, iostream.h
19. Fork,Kill function
20. Compiler converts letters to binary code at one go.

Solution for running executables in PHP | (for version `GLIBCXX_3.4.21' not found)

Sun, 19 Nov 2017 16:06:36 +0000

Just run the following:

sudo mv /opt/lampp/lib/libstdc++.so.6 /opt/lampp/lib/libstdc++.so.6.orig

and you should be good to go.

Never allow www-data user to bypass the password or you might be allowing security breaches.

P.S. This post is not going to be useful for most of the community here, but still there might be some it could be useful for.

Change Header of fastq files | awk one liner

Fri, 08 Sep 2017 11:27:30 +0000

Use the following awk for changing the header of the fastq files:

awk '{print (NR%4 == 1) ? "@1_" ++i : $0}' filename.fastq

Here the bold 1 can be changed to whatever string you wish to use.

PhD in Bioinformatics - list of Indian Institutes

Tue, 08 Aug 2017 06:22:04 +0000

Please add to this list of institutes which provide a PhD in Bioinformatics (specifically) so that a comprehensive list can be prepared.

Allahabad University
Amity University
Anna University, Chennai
Bharathidasan University, TamilNadu
Banasthali University, Rajasthan
Bose Institute, Kolkata
Calcutta University
Central University of South Bihar, Gaya
Dr. D.Y. Patil Biotechnology and Bioinformatics Institute, Pune
IBAB, Bangalore
IIIT Allahabad
IIIT Delhi
IIIT Hyderabad
Jaypee University of Information Technology, Solan, Himachal Pradesh
JNU, New Delhi (PhD in Life Science)
Karunya University, Tamil Nadu
National Institute of Technology, Bhopal
North-Eastern Hill University(NEHU), Shillong
Pondicherry University
Sastra University,Tamil Nadu
Shiv Nadar University, Noida
SHUATS, Allahabad
University of Hyderabad
University of Pune
WBUT, (MAKAUT) Salt Lake, Kolkata

M tech biotechnology after bsc

Wed, 05 Jul 2017 15:46:45 +0000

Sir I want ans....I am confused that we can m tech biotechnology after bsc
..its is my que we can do m tech biotechnology after bsc biotechnology

Starting Bioinformatics

Thu, 25 May 2017 03:18:09 +0000

Hello everyone. I have recently just taken interest in a career in computer science more specifically I want to get into Bioinformatics. I really find the idea of working in this field exciting but I feel as if I have no direction, no guide to show me what I should do to prepare myself. This semester I took my first programming class, C++, and it was pretty awesome. I wasn't the best but I did okay and got the gist of it. I had never heard of Bioinformatics until this class a few months ago, and Biology was my second choice of major besides CS so naturally I got pretty excited about it. What I would like to know is where can I go to find out more about Bioinformatics? What programming language should I learn? (I heard python is used a lot). What are some good books for a beginner? Also are there any little Bioinformatics programs I can make and mess around with using a c++ compiler? I am eager and ready for some knowledge and direction from experienced programmers who do this everyday. Thank you for reading and any replies and constructive criticism are welcomed. Cheers.

Parexel

Tue, 23 May 2017 14:03:45 +0000

Hello Sir! I have just completed my BSc in Bio-info. Now i am preparing for MSc. in Bio-info. Sir i want to know about Parexel. I want to work at Parexel. How do we get in there?

Ruchita

Mon, 22 May 2017 11:11:01 +0000

Hello, I am first year B.tech in biotechnology student. Please suggest to me, Is this proper timing for preparing for gate??

Training in bioinformatics

Mon, 15 May 2017 16:38:12 +0000

Myself a third year student of B.tech Biotechnology.
I have Some interest in the bioinformatics feild.
I have planned to learn a programming language like biopearl,biojava or python etc. in summer training and then planned to do a project in bioinformatics.

Possibly will be going for m.tech in future so if in future I wish tag my area of interest as "bioinformatics" so there during admission time/interview will this be accpetable or is an wet lab work also compulsary?

PERL Program - BINC 2017 question

Tue, 25 Apr 2017 05:18:37 +0000

Question:

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.

Solution:

#!/usr/bin/perl -w
# Perl program to calculate intra molecular distance
use strict;
my ($file,$line,@array_x,@array_y,@array_z,$dist,$j,$i,$element);
my $k=0;
print "Enter the PDB filename: ";
$file = ;
chomp $file;
open (FILE, $file) or die "Cannot open file $file \n\n" ;

while ($line = )
{
if ($line =~ /^ATOM/)
{
$array_x[$k] = (split (/\s+/, $line))[6];
$array_y[$k] = (split (/\s+/, $line))[7];
$array_z[$k] = (split (/\s+/, $line))[8];
$k++;
}
}
close FILE;
#print "K=$k \n";
#print "@array_x \n @array_y \n @array_z \n";
print "\n Intramolecular Distance Matrix is : \n\n";
print "ATOMi \t ATOMj \t Euclidean Distance \t Element \n";
for($i = 0; $i < $k ; $i++)
{
for($j = 0; $j < $k ; $j++)
{
#Euclidean Distance Calculation
$dist = sqrt(
($array_x[$i] - $array_x[$j])**2 +
($array_y[$i] - $array_y[$j])**2 +
($array_z[$i] - $array_z[$j])**2
);
if ($dist >= 6)
{
$element = 1;
print "$i \t $j \t $dist \t $element \n";
}
else
{
$element = 0;
print "$i \t $j \t $dist \t $element \n";
}
}
}