BOL: Related items

OMTools: a software package for visualizing and processing optical mapping data

BioJoker — Fri, 29 Mar 2019 01:21:54 -0500

OMTools, an efficient and intuitive data processing and visualization suite to handle and explore large-scale optical mapping profiles. OMTools includes modules for visualization (OMView), data processing and simulation. These modules together form an accessible and convenient pipeline for optical mapping analyses.

https://github.com/TF-Chan-Lab/OMTools

Address of the bookmark: https://github.com/TF-Chan-Lab/OMTools

BIC-PGI Bioinformatics Project Dissertation Program

Fri, 12 Dec 2014 21:17:30 -0600

Biomedical Informatics Centre, PGIMER, Chandigarh invites application for a project dissertation program for students who have completed their first year of M.Sc. in Bioinformatics.

This is an exciting opportunity for Master's students to train in modern methods in Bioinformatics. The duration of the training will be four to six months, starting from January 2015.

Education: Pursuing M.Sc. Bioinformatics

Essential: Post graduate applicants should have completed their first year and should be in the third semester or first half of the second year.

Only students who are willing to spend a minimum period of 4 months to a maximum of six months, without any break, would be eligible for the program.

How to Apply: Candidates interested in the above project dissertation program should apply online.

Send your CV, Scanned copy of letter of recommendation from Head of Institution along with Registration form in the given format should be sent to: info@bicpgi.org

Please mention clearly “Project dissertation & your Name” in the Subject.

The last date for application is December 31, 2014

Note: Selected candidates may please note that the program is free of cost and would not provide any financial aid for transport and stay.

Name of the selected candidates would be posted on the centre website by December 31, 2014. Incomplete applications will be rejected.

For more information visit our website: http://www.bic-pgi.org/project_dissertation.pdf

VCF2PopTree: a client-side software to construct population phylogeny from genome-wide SNPs

Surabhi Chaudhary — Sat, 25 Dec 2021 00:13:31 -0600

VCF2PopTree is a client-side software written in Javascript and it runs purely within the user’s computer/browser. VCF2PopTree is compatible with all population browsers including Chrome, Opera, Edge and Firefox and works equally efficient in Mac, Windows and Linux (Ubuntu).

Furthermore, it displays the tree in a mobile phone (iPhone and Android) if the input file size is small. CITATION: Subramanian, S., Ramasamy, U. and Chen, D. (2019). VCF2PopTree: a client-side software to construct population phylogeny from genome-wide SNPs. Peer J. x:yy.

Address of the bookmark: https://github.com/sansubs/vcf2pop

dna2bit: an ultra-fast and accurate genomic distance estimation software

LEGE — Sun, 31 Aug 2025 06:24:58 -0500

dna2bit is a software tool developed in C++11, leveraging the capabilities of OpenMP for parallel computing and the popcount technique for efficient bit manipulation. It has been thoroughly tested using the g++ and clang compilers on both Linux and MacOS platforms.

Address of the bookmark: https://github.com/lijuzeng/dna2bit

MIT Computational Biology Group

Thu, 18 Dec 2014 14:47:01 -0600

My research group consists primarily of computer science graduate students and postdocs with expertise in algorithms, statistical inferences and machine learning, and sharing a passion for understanding fundamental biological problems.

We work in a highly interdisciplinary environment at the interface of Computer Science and Biology. Since its inception, our lab has eagerly engaged in collaborative research partnerships with biological and experimental collaborators, facilitated by our affiliation with the Broad Institute and the Computational and Systems Biology initiative (CSBi) at MIT, our participation in the Epigenome Roadmap, ENCODE, and modENCODE consortia, and by several other ongoing collaborations at MIT, Harvard, and the Harvard Medical School affiliated hospitals.

http://compbio.mit.edu/

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”

Bioinformatics Scientist at ICAR Labs

Sun, 21 Dec 2014 23:47:03 -0600

AGRICUL AGRICULTURAL SCIENTISTS RECRUITMENT BOARD TURAL SCIENTISTS RECRUITMENT BOARD
KRISHI ANUSANDHAN BHAVAN-I, PUSA, NEW DELHI-110 012

ADVERTISEMENT NO. 03/2014

PRINCIPAL SCIENTIST

Pay Band: Minimum pay of `43,000 in the PB-4 of `37400-67000/- + RGP of `10,000/-.

Age: The candidates must not have attained the age of 52 years as on 19.01.2015. There shall be no age limit for the Council’s employees.

ICAR-Indian Institute for Agricultural Biotechnology, (IIAB) Ranchi (Jharkhand)

151. Principal Scientist (Bioinformatics) (One post)

SENIOR SCIENTIST/PROGRAMME COORDINATOR

Pay Band: PB-4 of ` 37400-67000/- + RGP of ` 9,000/-.

Age: The candidates must not have attained the age of 47 years as on 19.01.2015. There shall be no age limit for the Council’s employees.

National Institute of Biotic Stress Management, Raipur (Chhattishgarh)

166. Senior Scientist (Bioinformatics) (One post)

IMPORTANT NOTE
I. (i) CLOSING DATE

THE CLOSING DATE FOR RECEIPT OF APPLICATIONS IN AGRICULTURAL SCIENTISTS RECRUITMENT BOARD IS 19.01.2015 (For applications posted from abroad and in the Andaman and Nicobar Islands, Lakshdweep, Minicoy and Amindivi islands, States/ Union Territories in the North-Eastern Region, Ladakh Division of J & K State, Sikkim, Pangi, Sub-division of Chamba, Lahul and Spiti Districts of Himachal Pradesh, the last date for receipt of application will be 02.02.2015). Non receipt of the application by the closing date will result in rejection of the application.

More Info: http://asrb.org.in/administrator/uploads_dir/1418978057english.pdf

Scallop: reference-based transcriptome assembler for RNA-seq

Rahul Nayak — Tue, 08 May 2018 04:23:27 -0500

Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts. Scallop achieves this improvement through a novel algorithm that can be proved preserving all phasing paths from reads and paired-end reads, while also achieves both transcripts parsimony and coverage deviation minimization.

Scallop paper has been published at Nature Biotechnology. The datasets and scripts used in this paper to compare the performance of Scallop and other assemblers are available at scalloptest.

Please also checkout the podcast about Scallop (thanks Roman Cheplyaka for the interview). It is available at both the bioinformatics chat and iTunes.

https://github.com/Kingsford-Group/scallop

Address of the bookmark: https://github.com/Kingsford-Group/scallop

gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output

Rahul Nayak — Fri, 24 Jan 2020 06:04:40 -0600

gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. They compare the performance of gapFinisher against two other published gap filling tools PBJelly and GMcloser.

gapFinisher can fill gaps in draft genomes quickly and reliably.

Address of the bookmark: https://github.com/kammoji/gapFinisher

Which of the followings are the best place to study Bioinformatics ?

Reshma Khatun — Sun, 28 Dec 2014 00:20:30 -0600

Bioinformatics is a major growth area and qualified Bioinformaticians are in high demand. An explosion in biological data has resulted from genome projects, next generation sequencing and other 'omics' techniques. Bioinformatics provides the tools to analyse and exploit such data sets.

Can you please suggest me the best place to study bioinformatics ( Grad/PostGrad).