BOL: Related items

Bioinformatics tools for genome assembly !

BioStar — Mon, 24 Jul 2023 07:04:26 -0500

There are numerous genome assembly tools available, each with its strengths and weaknesses. Here is a list of some widely used genome assembly tools as of my last update in September 2021:

SPAdes: An assembler specifically designed for single-cell and multi-cell bacterial genomes, as well as small eukaryotic genomes.
ABySS: A parallelized assembler for large genomes that uses de Bruijn graphs.
Velvet: Another de Bruijn graph-based assembler optimized for short-read sequencing data.
SOAPdenovo: A de Bruijn graph-based assembler designed for short reads, widely used for assembling large and complex genomes.
MaSuRCA: A hybrid assembler that combines data from multiple sequencing technologies, such as Illumina and PacBio.
Canu: A long-read assembler optimized for PacBio and Oxford Nanopore sequencing data.
Flye: A long-read assembler suitable for bacterial and small eukaryotic genomes.
SMARTdenovo: An assembler designed for long reads, particularly suited for PacBio data.
SPAdes Long Read (SPAdesLR): An extension of SPAdes for long-read data, such as those from PacBio or Nanopore.
Minia: An assembler optimized for low memory consumption, suitable for small and medium-sized genomes.
Unicycler: A hybrid assembler that combines short and long reads for circular bacterial genome assembly.
wtdbg2: A de Bruijn graph assembler for long reads, efficient for very large genomes.
Shasta: A long-read assembler that uses the Overlap-Layout-Consensus approach, suitable for PacBio and Nanopore data.
Sparc: An assembler designed to handle noisy long reads from Nanopore sequencing.
CANA: An assembler for metagenomic data, particularly for complex and diverse microbial communities.
Ra Assembler: A metagenome assembler for long reads, designed for highly complex metagenomic samples.

Please note that the field of bioinformatics is constantly evolving, and new assembly tools may have emerged since my last update. Additionally, the performance of these tools can vary depending on the characteristics of the sequencing data and the genome being assembled. When selecting an assembly tool, consider the specific requirements of your project, the available data types, and the computational resources at your disposal. Always refer to the respective tool's documentation and publications for the most up-to-date information and recommendations.

BioKit: a set of tools dedicated to bioinformatics, data visualisation

Neel — Tue, 18 Jun 2024 02:04:39 -0500

BioKit is a set of tools dedicated to bioinformatics, data visualisation (biokit.viz), access to online biological data (e.g. UniProt, NCBI thanks to bioservices). It also contains more advanced tools related to data analysis (e.g., biokit.stats). Since R is quite common in bioinformatics, we also provide a convenient module to run R inside your Python scripts or shell (:mod:biokit.rtools module).

Address of the bookmark: https://biokit.readthedocs.io/en/latest/index.html

Phytozome v12.1: plant science community hub for accessing palnts genomic data

Surabhi Chaudhary — Tue, 17 Mar 2020 07:30:17 -0500

Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as selected genomes and datasets that have been sequenced elsewhere. As of release v12.1.6, Phytozome hosts 93 assembled and annotated genomes, from 82 Viridiplantae species. More than half of these genomes have been sequenced, assembled and/or annotated with JGI Plant Science program resources. By integrating this large collection of plant genomes into a single resource and performing comprehensive and uniform annotation and analyses, Phytozome facilitates accurate and insightful comparative genomics studies.

Address of the bookmark: https://phytozome.jgi.doe.gov/pz/portal.html

A History of Bioinformatics (in the Year 2039)

Wed, 23 Jul 2014 06:37:51 -0500

C. Titus Brown http://video.open-bio.org/video/1/a-history-of-bioinformatics-in-the-year-2039

Nataša Pržulj Lab

Fri, 30 Aug 2013 06:29:17 -0500

Nataša Pržulj Lab's research involves applications of graph theory, mathematical modeling, and computational techniques to solving large-scale problems in computational and systems biology.They are interested in computational and theoretical solutions to practical problems in many areas of systems biology, planar cell polarity, proteomics, cancer informatics, and drug discovery and design.

More at http://www.doc.ic.ac.uk/~natasha/index.html

RA Bioinformatics at NII

Thu, 22 Oct 2015 01:56:26 -0500

NATIONAL INSTITUTE OF IMMUNOLOGY

NEW DELHI-110067

Applications are invited for the position of Research Associate (RA) for the following time-bound sponsored project as per the details given below:

1. BTIS project entitled, “National Infrastructural Facility in the Area of Immunology” funded by DBT

Research Associate (One Position only)

Dr. Debasisa Mohanty Staff Scientist-VI deb@nii.res.in

Educational Qualifications: Ph.D in Bioinformatics or Biological Sciences or Biotechnology with research experience and publication record in indexed peer reviewed journals in the area of bioinformatics or computational biology.

Emoluments: The selected candidates will draw consolidated emoluments as per Institute Rules, depending upon qualifications & experience Research Associate: Rs. 36,000/- per month plus 30% HRA

Job description & Desired Knowledge: The candidate should be well versed in Programming in PERL/C++, HTML, CGI, web sever and portal development, computational analysis of protein structure & function, molecular dynamics simulations and use of high performance computing systems.

General Terms & Conditions:-

1. The candidates selected for the above posts will be on contract for one year or duration of the project whichever is shorter, at a time.

2. No hostel/ housing facility will be provided.

3. Applicants may clearly mention the category they belong to i.e. SC/ST/OBC/PH and attach documentary proof of the same.

4. No TA/DA will be paid for attending the interview, if called for.

5. Apart from sending application in the prescribed format given below, candidates should send complete Curriculum Vitae along with the names of three referees. Curriculum Vitae should contain details of the experimental expertise and list of publications. 6. Canvassing in any form will be a disqualification.

HOW TO APPLY Interested candidates may apply directly, STRICTLY IN THE PRESCRIBED FORMAT GIVEN BELOW, through e-mail, to the Investigator of the project, clearly indicating the name of the project along with their complete C.V., Email ID, fax numbers, telephone numbers. Only Short listed candidates will be called for interview and they required to submit attested copies of all their certificates and a Demand Draft of Rs 100/- drawn on Canara Bank or Indian Bank payable at Delhi/New Delhi in favour of the Director, NII (SC/ST/PH and Women candidates are exempted from payment of fees) subject to submission of documentary proof), at the time of interview. (E-MAIL APPLICATIONS SHOULD MENTION BTIS-RA 2015 IN THE SUBJECT LINE)

LAST DATE OF RECEIPT OF APPLICATIONS: 29th October, 2015

www1.nii.res.in/sites/default/files/projectappointments-Dr.Mohanty-29oct2015.pdf

Genetic Test in India

Rahul Agarwal — Sun, 11 Aug 2013 10:54:35 -0500

1.Xcode Life Sciences Pvt. Ltd.
6B, Eldorado,
112, Nungambakkam High Road,
Nungambakkam, Chennai 600034
Tamil Nadu, India

2.Mapmygenome™
Royal Demeure,HUDA Techno Enclave,
Plot No. 12/2, Sector-1 500 081
Madhapur,Hyderabad
AP, India

3. DNA Labs India

http://www.dnalabsindia.com/lab.php

4.MedGenome Labs Pvt Ltd
(Division of SciGenom Labs Pvt Ltd.)
Plot no: 43A,SDF, 3rd floor
A Block,CSEZ, Kakanad, Cochin
Kerala - 682037
Phone: 0484 - 2413399
Fax: 0484 - 2413398
Email: info@medgenome.com

5.Narayana Nethralaya

Narayana Hrudayalaya Campus
Narayana Health City
# 258/A, Bommasandra, Hosur Road,
Bangalore - 560 099 - INDIA.
TEL: +91-80-66660655-0658
FAX: +91-80-66660650
Mobile: 9902 821128 (Emergency Only)
e-mail: info@narayananethralaya.com

6.BioAxis DNA Research Centre Private Limited
13-51,Sri Lakshmi Nagar colony,
Besides Big Bazar, Near Kamineni Hospitals
GSI Post BandalGuda (L B Nagar) Hydeabad-500068
Andhra Pradesh (India).
Phone : +91-40-24034503/+91-9246338983

7.Gene Guiide

8th Floor, Embassy Towers, 7 Bungalows Rd, Versova, Andheri West, Mumbai-61
09167 117799
info@geneguiide.com

See more at: http://www.geneguiide.com

8.INDIAN BIOSCIENCES
Regd. Office:
G-2 (Ground Floor Rear), Kailash Colony, New Delhi - 110048, India.
Phone: +91 (0)11 29236088, Email: info@inbdna.com.

9.SRL Limited

GP-26, MARUTI INDUSTRIAL ESTATE,

UDYOG VIHAR,SECTOR-18,

GURGAON - 122015

Tel: 0124-3001243 / 0124-3001209

SRL Limited
VASANT VIHAR, 8, PALAM MARG,
NEW DELHI - 110057
Tel: 011 - 4229 5333

Website: http://www.srlworld.com
National Customer care number:
Call Toll Free : 1800-222-660/1800-102-8282
E-mail id: customercare@srl.in

10.Tata Memorial Centre,

Advanced Centre for Treatment, Research and Education in Cancer

Kharghar, Navi Mumbai - 410 210, INDIA.

Tel: +91-22-2740 5000

Fax: +91-22-2740 5085

E-mail: mail@actrec.gov.in

Directional dominance on stature and cognition in diverse human populations

Rahul Agarwal — Sat, 11 Jul 2015 12:43:51 -0500

Analysis of the genomes of >350,000 individuals revealed the existence of a small though measureable association between genome-wide homozygosity and some vital complex traits...

Directional dominance is predicted for traits under directional evolutionary selection, this study provides evidence that increased stature and cognitive function have been positively selected in human evolution, whereas many important risk factors for late-onset complex diseases may not have been.

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14618.html

Address of the bookmark: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14618.html

The Centre for Bioinformatics (MCB) Lab

Sun, 14 Jul 2013 12:41:20 -0500

The Centre for Bioinformatics (MCB) is a diverse collection of professors, postdoctoral fellows, and students, who share a common interest in Bioinformatics.

Research Area

We are interested in the development of the statistics and computational methods for the analysis of this data in breast cancer.
We have worked on probabilistic models for subcellular localization, protein-protein interactions, and problems related to chemical genomics.
We are interested in the development of bioinformatics/biostatistical methodology in the analysis of epigenetic/epigenomic data.
We are interested in integrative bioinformatics approaches to learn the gene, gene products, interactions, and regulatory mechanisms involved in mental retardation.

Link @ http://www.mcgill.ca/mcb/

BioProgramming

Jitendra Narayan — Sun, 14 Jul 2013 16:29:53 -0500

The completion of the first human genome drafts was just a start of the modern DNA sequencing era which resulted in further invention, improved development toward new advanced strategies of high-throughput DNA sequencing, so called the “high-throughput next generation sequencing” (HT-NGS). The decreasing genome sequencing cost and desire to explore and understand biological machanism at genomic level, speed up the genomic sequencing projects. In the fast growing HT-NGS technologies, the main challenge is to cope with the analysis of vast production of sequencing database through advanced bioinformatics tools. In oder to develope sotware/tools bioinformatician/ biological programmers need to expertise in any one one the programming language. However, sometime one language are not enough to handle all sort of biological needs, which compel us to learn new biologically suitable language to handle ever growing genome or protein sequences.

The next step after reading genetic code is writing a script to analyse and explore the hidden information. This tutorial is aimed to introduce you new biological programming languages with their packages/libraries, and assist in your scripting work.

Navigate the sub-section of this page [ see right hand side of the page for it ]