BOL: Related items

Biotechnology Eligibility Test (BET) Question Paper !

Abhimanyu Singh — Wed, 17 Apr 2019 04:56:33 -0500

DBT-BET JRF 2019 Exam was held successfully on 14th April 2019. Official Question Paper & Answer key of DBT-BET 2019 Exam has been released.

The best part about the DBT-BET Exam is both the question paper & answer key is released immediately after the exam so you get the upper hand here to check how well you did in the DBT-BET exam, how much you are going to score and if you can pass the Exam with good score. This helps you in planning your career ahead.

DBT Exam is held once in a year by Department of Biotechnology – Govt of India. Candidates willing to get DBT-Junior Research Fellowship – DBT JRF fellowship should take up the DBT-BET Exam, DBT – Biotechnology Eligibility Test (BET) 2020 to be held on somewhere in the month of April. Official Notification for DBT-BET 2020 will be released in Feb 2020.

Answer at https://bioinformaticsonline.com/file/view/39262/biotechnology-eligibility-test-bet-answer-set

Scientists map 17,294 proteins produced in human body

Jit — Thu, 29 May 2014 01:57:55 -0500

Indian scientists missed the genomic profiling bus, but they've more than made up for it by creating the first human proteome map which is an extension of the genomic study. Till now, here is no direct equivalent for the human proteome. But recently two groups present mass spectrometry-based analysis of human tissues, body fluids and cells mapping the large majority of the human proteome.

The Indian scientists working in Bangalore, along with their American counterparts, have mapped more than 17,000 proteins in 30 organs of the human body. Just like the human genome was sequenced around the turn of the millennium, this is an equivalent mapping of the human proteome.

The researcher estimated there are around 20,500 proteins in the human body. These scientists have profiled around 17,294, which account for around 84% of the total proteins. Apart from this, the team also traced around 2,500 of 3,000 proteins that had been categorised as "missing proteins".

The work, done by group of Indian scientists, and Johns Hopkins University, published in the renowned journal Nature ( http://www.nature.com/nature/journal/v509/n7502/full/nature13302.html ). Of the 72 people who worked on the project, 46 are Indians.

Reference:

http://www.nature.com/nature/journal/v509/n7502/full/nature13302.html

http://www.proteinatlas.org/ -The antibody-based Human Protein Atlas programme

http://www.humanproteomemap.org/ -Proteogenomic analysis by identifying translated proteins from annotated pseudogenes, non-coding RNAs and untranslated regions.

https://www.proteomicsdb.org/ -Assembled protein evidence for 18,097 genes in ProteomicsDB

GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns

Neel — Sun, 15 Mar 2020 03:41:12 -0500

GSP4PDB is a user-friendly and efficient application to search and discover new patterns of protein-ligand interaction.

GSP4PDB is part of the services provided by the Bioinformatic Group of the University of Talca

http://gdblab.com/gsp4pdb/gsp4pdb2/

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3352-x

Address of the bookmark: http://gdblab.com/gsp4pdb/gsp4pdb2/

How to sequence the human genome - Mark J. Kiel

Fri, 30 May 2014 13:24:11 -0500

View full lesson: http://ed.ted.com/lessons/how-to-sequence-the-human-genome-mark-j-kiel Your genome, every human's genome, consists of a unique DNA sequence of A's, T's, C's and G's that tell your cells how to operate. Thanks to technological advances, scientists are now able to know the sequence of letters that makes up an individual genome relatively quickly and inexpensively. Mark J. Kiel takes an in-depth look at the science behind the sequence. Lesson by Mark J. Kiel, animation by Marc Christoforidis.

MinION_GC: An R script to do some QC on MinION data

Radha Agarkar — Sun, 03 Dec 2017 15:19:18 -0600

Other tools focus on getting data out of the fastq or fast5 files, which is slow and computationally intensive. The benefit of this approach is that it works on a single, small, .txt summary file. So it's a lot quicker than most other things out there: it takes about a minute to analyse a 4GB flowcell on my laptop.

https://github.com/roblanf/minion_qc

Address of the bookmark: https://github.com/roblanf/minion_qc

Genomics and Personalized Medicine

Sun, 01 Jun 2014 23:38:42 -0500

(October 20, 2009) Michael Snyder, Professor of Genetics and Chair of the Department of Genetics at Stanford, discusses advances in gene sequencing, the impact of genomics on medicine, the potential for personalized medicine. and efforts at Stanford to further study these issues. Stanford Mini Med School is a series arranged and directed by Stanford's School of Medicine, and presented by the Stanford Continuing Studies program. Featuring more than thirty distinguished, faculty, scientists and physicians from Stanford's medical school, the series offers students a dynamic introduction to the world of human biology, health and disease, and the groundbreaking changes taking place in medical research and health care. Stanford University http://www.stanford.edu Stanford University School of Medicine http://med.stanford.edu Stanford Continuing Studies http://continuingstudies.stanford.edu Stanford University Channel on YouTube: http://www.youtube.com/stanford

Tools and Method for Haplotype phasing !

Manisha Mishra — Fri, 04 Sep 2020 20:41:40 -0500

Huge amounts of genotype data are being produced with recent technological advances, both from increasingly comprehensive and inexpensive genome-wide SNP microarrays and from ever more accessible whole-genome and whole-exome sequencing methods. The vast amount of knowledge contained in these results, however, is best exploited through phased haplotypes, which classify the alleles co-located on the same chromosome. Since sequence and SNP array data normally take the form of unphased genotypes, one does not specifically observe which of the two parental chromosomes, or haplotypes, falls on a specific allele. Fortunately, new advances in both computational and laboratory methods promise improved determination of haplotype phase. Following are useful tools :

Arlequin: http://cmpg.unibe.ch/software/arlequin3/

BEAGLE: http://faculty.washington.edu/browning/beagle/beagle.html

fastPHASE: http://stephenslab.uchicago.edu/software.html

GENEHUNTER: http://linkage.rockefeller.edu/soft/gh/

The Genome Analysis Toolkit:

http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit

IMPUTE2: https://mathgen.stats.ox.ac.uk/impute/impute_v2.html

MACH: http://www.sph.umich.edu/csg/abecasis/MACH/

MERLIN: http://www.sph.umich.edu/csg/abecasis/Merlin/

PHASE: http://stephenslab.uchicago.edu/software.html

PL-EM: http://www.people.fas.harvard.edu/~junliu/plem/

“Read-backed phasing” algorithm: http://www.broadinstitute.org/gsa/wiki/index.php/Read-backed_phasing_algorithm

SHAPE-IT: http://www.griv.org/shapeit/

Adhoc Bioinformatics Faculty Position @ NIT

Tue, 03 Jun 2014 16:19:52 -0500

NATIONAL INSTITUTE OF TECHNOLOGY, DEPARTMENT OF BIOTECHNOLOGY, WARANGAL – 506 021, Andhra Pradesh

No.NITW/BT/2014/adhoc

APPLICATIONS ARE INVITED FOR THE APPOINTMENT OF ADHOC FACULTY ON CONTRACT BASIS IN THE DEAPARTMENT OF BIOTECHNOLOGY

Period of Contract: Initially the appointment is for one semester i.e., from July 2014 up to December 2014 only.

Essential Qualifications:

i) B. Tech or equivalent in Biotechnology/ Industrial Biotechnology/ Biochemical Engineering / Chemical Engg. Or M. Sc in Microbiology/ Botany/ Zoology/ Biochemistry/Biotechnology and ii) M. Tech or equivalent in Biotechnology/Industrial Biotechnology/Bioinformatics

Integrated M. Tech in Biotechnology/Industrial Biotechnology/ Bioinformatics

Candidates must possess First class (60% aggregate marks or 6.5 CGPA) at B. Tech/ M. Sc and M. Tech.

Desirable: Ph. D Pay Package: All selected candidates shall be eligible for a consolidated pay of Rs.30, 000/- per month. Candidates with Ph. D shall be eligible for an additional amount of Rs.5, 000/- per month.

How to apply : Applications on plain paper with attested photocopies of certificate and bio data along with justification for eligibility should reach to the Head, Department of Biotechnology, National Institute of Technology, Warangal AP 506004 in the form of soft or hard copy on or before 21st June 2014 email : biotech_hod@nitw.ac.in

Intimation: No separate call letters will be sent to the candidates. All the eligible candidates will be notified in the institute web site on 23rd June 2014. All the eligible candidates are requested to report for the interview to the Head, Department of Biotechnology at 9:00 AM on 27th June 2014

Joining: Selected candidates will be informed and they are expected to join immediately.

http://www.nitw.ac.in/nitw/announcements/2014/Bio-Adhoc%20Advt.%20May-2014.pdf

Tools to Predict the Impact of Missense Variants !

Jit — Mon, 23 Apr 2018 12:57:33 -0500

Prioritizing missense variants for further experimental investigation is a key challenge in current sequencing studies for exploring complex and Mendelian diseases. A large number of in silico tools have been employed for the task of pathogenicity prediction, including PolyPhen‐2, SIFT, FatHMM, MutationTaster‐2, MutationAssessor, Combined Annotation Dependent Depletion, LRT, phyloP, and GERP++, as well as optimized methods of combining tool scores, such as Condel and Logit. Due to the wealth of these methods, an important practical question to answer is which of these tools generalize best, that is, correctly predict the pathogenic character of new variants.

Study of 10 tools on five datasets that such a comparative evaluation of these tools is hindered by two types of circularity: they arise due to (1) the same variants or (2) different variants from the same protein occurring both in the datasets used for training and for evaluation of these tools, which may lead to overly optimistic results. Comparative evaluations of predictors that do not address these types of circularity may erroneously conclude that circularity confounded tools are most accurate among all tools, and may even outperform optimized combinations of tools.

Following tools are useful for mis sense muation detection ...

PolyPhen‐2 (PP2)
“Predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations”

MutationTaster‐2 (MT2)
“Evaluation of the disease‐causing potential of DNA sequence alterations”

MutationAssessor (MASS)
“Predicts the functional impact of amino acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms”

LRT
“Identify a subset of deleterious mutations that disrupt highly conserved amino acids within protein‐coding sequences, which are likely to be unconditionally deleterious”

SIFT
“Predicts whether an amino acid substitution affects protein function”

GERP++
“Identifies constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not occur because the element has been under functional constraint. We refer to these deficits as “rejected substitutions.” Rejected substitutions are a natural measure of constraint that reflects the strength of past purifying selection on the element”

phyloP
“Compute conservation or acceleration P values based on an alignment and a model of neutral evolution”

FatHMM unweighted (FatHMM‐U)
Predicts “functional consequences of both coding variants, that is, nonsynonymous single‐nucleotide variants, and noncoding variants”

FatHMM weighted (FatHMM‐W)
Predicts “functional consequences of both coding variants, that is, nonsynonymous single‐nucleotide variants, and noncoding variants” and its weighting scheme attributes higher tolerance scores to SNVs in proteins, related proteins, or domains that already include a high fraction of pathogenic variantsh

Combined Annotation Dependent Depletion (CADD)
“CADD is a tool for scoring the deleteriousness of single‐nucleotide variants as well as insertion/deletions variants in the human genome”

Search Shell Command History

Rahul Nayak — Thu, 12 Jun 2014 17:43:34 -0500

We use couple of hundreads of command in daily basis. Most of them are actually repeated several time. The question remain open how do I search old command history under bash shell and modify or reuse it?

Now a days almost all modern shell allows you to search command history if enabled by user. Use history command to display the history list with line numbers. Lines listed with with a * have been modified by user.

Shell history search command

Type history at a shell prompt:
$ history

It will display the list of all used commandline history with an serial number.

To search particular command, enter:
$ history | grep command-name
$ history | egrep -i 'scp|ssh|ftp'
Emacs Line-Edit Mode Command History Searching

To get previous command containing string, hit [CTRL]+[r] followed by search string:

(reverse-i-search):

To get previous command, hit [CTRL]+[p]. You can also use up arrow key.

CTRL-p

To get next command, hit [CTRL]+[n]. You can also use down arrow key.

CTRL-n

fc command

Apart from hostory command there are fc command to extract the command from history. The fc stands for either "find command" or "fix command.

For example list last 10 command, enter:
$ fc -l 10
To list commands 130 through 150, enter:
$ fc -l 130 150
To list all commands since the last command beginning with ssh, enter:
$ fc -l ssh
You can edit commands 1 through 5 using vi text editor, enter:
$ fc -e vi 1 5

Delete command history

The -c option causes the history list to be cleared by deleting all of the entries:
$ history -c