BOL: Related items

320000 viruses in mammals yet to sequenced in future!!!

Rahul Agarwal — Tue, 03 Sep 2013 08:35:30 -0500

With current biological technique improvements, finally it is now possible to look at millions of unknown viruses at genomic level and understand the mechanism. According to available data, close to 70 per cent of emerging viral diseases such as HIV/AIDS, West Nile, Ebola, SARS, and influenza, are zoonoses - infections of animals that cross into humans.

To address the challenges of describing and estimating virodiversity, a team of investigators from Center for Infection and Immunity (CII) and EcoHealth Alliance began in jungles of Bangladesh - home to the flying fox.

Reference:

http://economictimes.indiatimes.com/news/news-by-industry/et-cetera/mammals-harbour-at-least-320000-new-viruses/articleshow/22253268.cms

http://www.bbc.co.uk/news/science-environment-23932400

Submit your SARS-CoV-2 sequence data to GenBank

Neel — Thu, 09 Apr 2020 18:28:25 -0500

Submit your SARS-CoV-2 sequence data to GenBank and SRA with our new submission landing page. Submission is simple and streamlined *and* there’s a rapid turnaround. https://submit.ncbi.nlm.nih.gov/sarscov2/

Quickly and easily add your SARS-CoV-2 sequence data to the growing public archive with new, special features and support from NCBI. new SARS-CoV-2 sequence submission landing page will help you get started. GenBank submissions are accessioned and released in approximately 1-2 working days, and Sequence Read Archive (SRA) submissions typically processed and released within hours. Submission is simple!

More information is available on NCBI Insights. https://ncbiinsights.ncbi.nlm.nih.gov/2020/04/09/sars-cov2-data-streamlined-submission-rapid-turnaround/

Mosquito species known for transmitting the Dengue virus

BioStar — Wed, 03 Apr 2024 00:05:51 -0500

Here is a list of mosquito species known for transmitting the Dengue virus along with essential and applied information about each species:

1. Aedes aegypti:
- Geographical Distribution: Found in tropical and subtropical regions worldwide.
- Biting Behavior: Daytime biter, prefers feeding indoors, often around human dwellings.
- Role in Dengue Transmission: Primary vector responsible for transmitting Dengue virus to humans.

2. Aedes albopictus (Asian tiger mosquito):
- Geographical Distribution: Found in tropical, subtropical, and temperate regions worldwide.
- Biting Behavior: Daytime biter, feeds both indoors and outdoors, aggressive feeder.
- Role in Dengue Transmission: Secondary vector, can transmit Dengue virus to humans.

3. Aedes polynesiensis:
- Geographical Distribution: Found in Pacific Islands and coastal regions.
- Biting Behavior: Daytime biter, prefers feeding outdoors, often near coastal areas.
- Role in Dengue Transmission: Vector of Dengue virus in specific geographic regions.

4. Aedes scutellaris:
- Geographical Distribution: Found in Southeast Asia, Pacific Islands, and coastal regions.
- Biting Behavior: Daytime feeder, active in shaded areas, prefers outdoor environments.
- Role in Dengue Transmission: Vector of Dengue virus, particularly in coastal areas.

5. Aedes africanus:
- Geographical Distribution: Found in parts of Africa, including forested areas.
- Biting Behavior: Daytime feeder, prefers shaded areas, bites humans and other animals.
- Role in Dengue Transmission: Vector of Dengue virus in African regions.

Understanding the geographical distribution and biting behavior of these mosquito species is crucial for implementing effective control and prevention strategies to reduce Dengue virus transmission.

Influenza animation - flu virus mechanism

Thu, 17 Oct 2013 19:43:13 -0500

Animation of the mechanism of an influenza virus and how Crucell's antibodies target the HA1 proteins on the virus and prevent further spread of influenza. Client: Crucell Direction, Design & Animation: Daniel Lim, 2Preform Music & Sound Design: Javier Barrero, Logical Disorder Production Company: David Hager, All Terrain Media

Frequently used bioinformatics tools for viral genome analysis !

Neel — Wed, 23 Jun 2021 07:40:41 -0500

IVA: accurate de novo assembly of RNA virus genomes.
Hunt M, Gall A, Ong SH, Brener J, Ferns B, Goulder P, Nastouli E, Keane JA, Kellam P, Otto TD.
Bioinformatics. 2015 Jul 15;31(14):2374-6. doi: 10.1093/bioinformatics/btv120. Epub 2015 Feb 28.

Adapter sequences:
Optimal enzymes for amplifying sequencing libraries.
Quail, M. a et al. Nat. Methods 9, 10-1 (2012).

GAGE:
GAGE: A critical evaluation of genome assemblies and assembly algorithms.
Salzberg, S. L. et al. Genome Res. 22, 557-67 (2012).

KMC:
Disk-based k-mer counting on a PC.
Deorowicz, S., Debudaj-Grabysz, A. & Grabowski, S. BMC Bioinformatics 14, 160 (2013).

Kraken:
Kraken: ultrafast metagenomic sequence classification using exact alignments.
Wood, D. E. & Salzberg, S. L. Genome Biol. 15, R46 (2014).

MUMmer:
Versatile and open software for comparing large genomes.
Kurtz, S. et al. Genome Biol. 5, R12 (2004).

R:
R: A language and environment for statistical computing.
R Core Team (2013). R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/.

RATT:
RATT: Rapid Annotation Transfer Tool.
Otto, T. D., Dillon, G. P., Degrave, W. S. & Berriman, M. Nucleic Acids Res. 39, e57 (2011).

SAMtools:
The Sequence Alignment/Map format and SAMtools.
Li, H. et al. Bioinformatics 25, 2078-9 (2009).

Trimmomatic:
Trimmomatic: A flexible trimmer for Illumina Sequence Data.
Bolger, A. M., Lohse, M. & Usadel, B. Bioinformatics 1-7 (2014).

Monkeypox virus isolate MPXV_USA_2022_MA001, complete genome

Jit — Tue, 26 Jul 2022 06:21:07 -0500

LOCUS       ON563414              197205 bp    DNA     linear   VRL 30-MAY-2022
DEFINITION  Monkeypox virus isolate MPXV_USA_2022_MA001, complete genome.
ACCESSION   ON563414
VERSION     ON563414.3
KEYWORDS    .
SOURCE      Monkeypox virus (monkeypox)
  ORGANISM  Monkeypox virus
            Viruses; Varidnaviria; Bamfordvirae; Nucleocytoviricota;
            Pokkesviricetes; Chitovirales; Poxviridae; Chordopoxvirinae;
            Orthopoxvirus.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/nuccore/ON563414

Exchange Programme for Indian scientist !!

Shruti Paniwala — Wed, 18 Dec 2019 21:11:22 -0600

The Indian National Science Academy (INSA) is a premier scientific learned body (established in 1935) representing all branches of science –Physical and Biological Sciences including Engineering, Medicine and Agricultural Sciences. The Academy has been promoting scientific cooperation with Academies/Organisations of several countries the world over. The Academy has links with the Academies and Organisations in Asia, Europe
and South America. These programmes provide opportunities to scientists working in various scientific institutions and organizations in the country for exchange of ideas, knowledge, establish new links, strengthen old links and undertake joint projects with their research partners in leading laboratories and institutions abroad.

The Academy has an International Exchange Programme with Academies/Organizations in the countries: Brazil, China, France, Hungary, Iran, Israel, Nepal, Philippines, Poland, Scotland, Slovak Republic, Republic of Slovenia, Sudan and Taiwan.

Applications are invited from Indian Nationals for consideration by the Academy for the next calendar year.

The applicant should be a scientist holding a regular (permanent) position in a recognized S & T Institution/University and actively engaged in research work in frontline areas.
He/She should not have been abroad during the last 3 years under any INSA Programme.
The scientist should have been accepted to work in an Institute/Laboratory in the country to be visited and this should be supported by a letter of invitation from the host abroad.
Those who wish to visit abroad for three months should submit a detailed programme of their collaborative research work to be conducted.

All applications duly completed should be forwarded to the academy through proper channel by the employer/head of the Institute.

Scientists selected for deputation abroad would be provided 100% travel support (by only Air India excursion class airfare, through shortest route from the place of duty in India to the nearest airport of host Institute and back) by INSA.
Medical Insurance purchased in India.
Visa fee (if any).
The receiving Academy/Organization would provide local hospitality including internal travel abroad.

Contact for detail at

www.insaindia.res.in

INDIAN NATIONAL SCIENCE ACADEMY
Bahadur Shah Zafar Marg, New Delhi – 110 002.
Telephone: 91-11-23221931 – 23221950 (EPABX),
Fax: 91-11- 23235648, 23231095

2.4 Mb Genome Size for World's Biggest Virus

Jitendra Narayan — Thu, 08 Aug 2013 10:05:37 -0500

The genome size of new discovered Pandoraviruses have roughly twice the size of the record-holding Megavirus genomic code. Interestingly only 6 percent of its genes resembled the genes other organisms. It is assume that it may come from a different origin.

For detail : http://www.sciencemag.org/content/341/6143/281

http://www.npr.org/blogs/health/2013/07/18/203298244/worlds-biggest-virus-may-have-ancient-roots

Virus 3D Animation

Sat, 26 Oct 2013 09:01:27 -0500

piranha.dl facebook site: http://www.facebook.com/home.php?#!/pages/piranhadl-3D/131721586891915

QuasiModo - Quasispecies Metric Determination on Omics

Neel — Sat, 26 Jun 2021 15:22:56 -0500

This repository contains the scripts and pipeline that reproduces the results of the HCMV benchmarking study. In this study we evaluated genome assemblers and variant callers on 10 in vitro generated, mixed strain HCMV sequence samples, each consisting of two lab strains in different abundance ratios. This tool can also be used to evaluate assemblies and variant calling results on other similar datasets.

https://academic.oup.com/bib/article/22/3/bbaa123/5868070

Address of the bookmark: https://github.com/hzi-bifo/Quasimodo