BOL: Related items

Walk-ins for JRF ans SRF post in NIRRH, Mumbai

Thu, 28 May 2015 19:04:57 -0500

Title of project- "EXPLORING THE HINGE AND TRANSMEMBRANE REGION OF HUMAN FSHR FOR DESIGN OF SMALL MOLECULE AND PEPTIDOMIMETIC MODULATORS"
Name of the Post- Junior Research Fellow
No. of vacancy- One
Stipend- Rs. 25000/ +30% HRA
Essential qualification- Candidate should be Post Graduate Degree in Life Sciences / Bioinformatics /Pharmacology/ Chemistry or any other relevant area of Biology or Graduate Degree in Professional Course with NET qualification or Post Graduate Degree in Professional Course.
Desirable- Candidate with Good knowledge of protein structures, docking, MD simulations will be preferred.
Age Limit- Not exceeding 28 Years
Duration of project- Upto May 2018

Title of project- "Analysis of the structures of known antimicrobial peptides using machine learning algorithms and molecular dynamics simulations".
Name of the Post- Senior Research Fellow
No. of vacancy- One
Stipend- Rs. 14000/ +30% HRA
Essential qualification- Candidate should be having M.Sc. degree in Life Sciences / Bioinformatics / Pharmacology/ Chemistry or any other relevant area of Biology and 2 years of research experience.
Desirable- Candidate with Good knowledge of protein structures, docking, MD simulations will be preferred.
Age Limit- Not exceeding 35 Years
Duration of project- Upto April 2016
How to Apply- Interested candidates can download the application form from below mentioned link- http://www.nirrh.res.in/links/BiodataForm.pdf
Candidate must bring the filled up application form along with all the relevant documents in original and one set of attested photocopies of the same and one passport size recent colour photograph.

Ref. - http://www.nirrh.res.in/links/job_jrf-srf.htm

Filtlong: quality filtering tool for long reads

Radha Agarkar — Wed, 13 May 2020 10:23:55 -0500

Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.

Filtlong builds into a stand-alone executable:

git clone https://github.com/rrwick/Filtlong.git
cd Filtlong
make -j
bin/filtlong -h

Address of the bookmark: https://github.com/rrwick/Filtlong

JRF Bioinformatics @ Pune University

Wed, 06 May 2015 06:21:09 -0500

Pune University is inviting applications from indian citizens for recruiting following posts:

Vacancies:
Junior Research Fellow-04
Age Limits:
Candidates age should be not more than 28 years.
Qualification:
Candidates should possess M.Sc in Microbiology/ Marine microbiology/Marine Biotechnology/ Bioinformatics/Zoology or equivalent degree with minimum 60% marks.
Selection Process:
Shortlisted candidates will be called for interview.
How to Apply:
Eligible candidates may send their applications in the prescribed format along with CV in an envelope should be superscribed as the "Application for the post of JRF" to Head Department of Zoology, Savitribai Phule Pune University on or before 10-05-2015.
Last Date:
10-05-2015

FastProNGS: fast preprocessing of next-generation sequencing reads

Rahul Nayak — Sat, 26 Dec 2020 08:35:21 -0600

FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by far the fastest.

Address of the bookmark: https://github.com/Megagenomics/FastProNGS

Affy has acquired Eureka Genomics for 15M $

Martin Jones — Wed, 20 May 2015 15:11:20 -0500

Affymetrix Acquires Assets Of Eureka Genomics Corporation To Provide High Throughput And Economical Crop And Animal Genotyping

http://www.thestreet.com/story/13151062/1/affymetrix-acquires-assets-of-eureka-genomics-corporation-to-provide-high-throughput-and-economical-crop-and-animal-genotyping.html

HairSplitter: assembling long reads in an unknown number of haplotypes

BioStar — Wed, 07 Dec 2022 00:13:40 -0600

Pros and cons of HairSplitter Limitations of HairSplitter:

Not very fast: it re-polishes the whole assembly

Limited in the number of haplotypes

Strengths of HairSplitter:

Very modular, can be used with any assembler

Naive: makes no assumption on ploidy, parameter-free

Safe: won’t artificially duplicate contigs

HairSplitter splits collapsed assemblies from “draft” assemblies obtained by any means

HairSplitter can recover haplotypes and distinguish repeated elements

Only needs sequencing reads, potentially error-prone

HairSplitter splits collapsed assemblies from “draft” assemblies obtained by any means

HairSplitter can recover haplotypes and distinguish repeated elements

Only needs sequencing reads, potentially error-prone

Not really available yet (github.com/RolandFaure/HairSplitter)

https://hal.archives-ouvertes.fr/hal-03864075/file/RolandFaure_presentation_SeqBIM_2022.pdf

Address of the bookmark: https://hal.archives-ouvertes.fr/hal-03817928/document

Alessandra Carbone Lab

Tue, 26 May 2015 08:54:34 -0500

Our group works on various problems connected with the functioning and evolution of biological systems. We use mathematical tools, coming from statistics and combinatorics, algorithmic tools and molecular physics tools to study basic principles of cellular functioning starting from genomic data. We run several projects in parallel, all aiming at understanding the basic principles of evolution and co-evolution of molecular structures in the cell. They are intimately linked to each other.

Our main research themes are:

Domain annotation and metagenomics
Transcriptomics and sequence analysis
Protein evolution and interactions
Protein conformational dynamics

More at http://www.lcqb.upmc.fr/AnalGenom/home.html

Jabba: Hybrid Error Correction for Long Sequencing Reads

Jit — Fri, 05 Jan 2018 03:58:14 -0600

Jabba is a hybrid error correction tool to correct third generation (PacBio / ONT) sequencing data, using second generation (Illumina) data.

Input

Jabba takes as input a concatenated de Bruijn graph and a set of sequences:

the de Bruijn graph should appear in fasta format with 1 entry per node, the meta information should be in the format:
>NODE
the set of sequences should be in fasta or fastq format. These sequences will be corrected (e.g. PacBio reads). The corrections will be written to a file Jabba fasta.
The output is a file in fasta format with corrections of the long reads, and additionally a file in the input format containing uncorrected reads.

https://github.com/biointec/jabba/wiki

https://almob.biomedcentral.com/articles/10.1186/s13015-016-0075-7

Address of the bookmark: https://github.com/biointec/jabba

X. Shirley Liu Lab

Tue, 26 May 2015 17:28:23 -0500

The research in our laboratories are focused on the following three areas:

Bioinformatics
Cancer
Epigenetics

More at http://liulab.dfci.harvard.edu/

Consed--A Finishing Package (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence)

Neel — Fri, 07 Feb 2020 07:16:22 -0600

Supports Illumina, 454, other Next-Gen and Sanger Reads and allows mixtures of these read types
Consed includes BamScape which can view bam files with unlimited numbers of reads. BamScape can bring up consed to edit reads and the reference sequence in targeted regions.
Consed is compatible with Newbler, Cross_match, Phrap, MIRA, Velvet and PCAP output.
Quickly takes the user to each variant site for viewing (also available as an automated report)
Overview of assembly can help detect and fix misassemblies
Editing time reduced by the program's ability to pin-point problem areas
Editing is guided by error probabilities

Address of the bookmark: http://www.phrap.org/consed/consed.html