BOL: Related items

Release Notes for Genome Workbench 2.10.5

Jit — Thu, 12 May 2016 13:49:41 -0500

New Features in latest release

New ProSplign tool integrated with Genome Workbench (Tutorial, Video)
New export function for BAM/cSRA coverage graphs (Tutorial)
New export function for alignments GFF3 format ((Tutorial))
Tree View: implemented new export mode based on selections (tutorial coming)
Tree View: added support for distance based circular trees
Tree View: new rooting mode (Midpoint Root) results in more balanced trees (Tutorial)
Tree View: added possibility to right-click on an edge between two nodes and "Place Root at Middle of Branch" – to re-root at mid-branch (Tutorial)

Entrez Direct: E-utilities on the UNIX Command Line

Anjana — Wed, 19 Oct 2016 08:06:24 -0500

Entrez Direct (EDirect) is an advanced method for accessing the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.

EDirect also provides an argument-driven function that simplifies the extraction of data from document summaries or other results that are returned in structured XML format. This can eliminate the need for writing custom software to answer ad hoc questions. Queries can move seamlessly between EDirect commands and UNIX utilities or scripts to perform actions that cannot be accomplished entirely within Entrez.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/books/NBK179288/

Eugene V. Koonin Lab

Tue, 09 Jan 2018 05:01:15 -0600

Interested in understanding the evolution of life. To obtain glimpses of such understanding, we employ existing and new methods of computational biology to perform research in several major areas.

https://www.ncbi.nlm.nih.gov/research/groups/koonin/

Magic-BLAST

Shruti Paniwala — Fri, 20 Mar 2020 15:18:36 -0500

Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-seq, locating the candidate introns and adding up the score of all exons. This is very different from other versions of BLAST, where each exon is scored as a separate hit and read-pairing is ignored.

Address of the bookmark: https://ncbi.github.io/magicblast/

NCBIBLAST+ 2.14.1 now available

Neel — Wed, 30 Aug 2023 02:36:13 -0500

#NCBIBLAST+ 2.14.1 now available with improved documentation, faster and more reliable database downloads, and some bug fixes.

Check out the changes they made.

They added the cleanup-blastdb-volumes.py script to remove unused BLAST database volumes. Read the documentation here.

They also switched the protocol from ftp to https to access BLAST databases for increased performance and reliability when downloading data from the NCBI with the update_blastdb.pl script.

And fixed a few bugs related to downloading data from the NCBI, and mt_mode crashing blastn and blastx.

Check out the release notes.

Download BLAST+ 2.14.1

Questions or comments? Please write the BLAST help desk.

More info and download: https://blast.ncbi.nlm.nih.gov/doc/blast-news/2023-BLAST-News.html

YOUR TURN THIS YEAR?

BioJoker — Fri, 17 May 2019 03:16:45 -0500

Apply for the Science & SciLifeLab Prize for Young Scientists — an annual prize awarded to early-career scientists. The prize is presented in four categories: Cell and Molecular Biology, Ecology and Environment, Molecular Medicine, and Genomics, Proteomics and Systems Biology.

The winners will have their essays published by Science, win up to USD 30,000 and be invited to Sweden to attend the award ceremony. Get ready for a life-changing moment in your scientific career.

Application deadline: July 15th, 2019

Eligible entrants must have been awarded their doctoral degree in 2017 or 2018. The winners from each category will compete for the Grand Prize.

Read more: scienceprize.scilifelab.se
Questions/Inquiries: SciLifeLabPrize@aaas.org

“It has absolutely brought a lot of exposure to me and to my research. I also think it went a long way in helping me to get my current position.”

Allison Cleary, 2015 Grand Prize Winner

“My advice for those thinking about applying for the Science and SciLifeLab Prize is to just go for it! It wasn’t the easiest thing trying to frame my work in a broader context, but in the end, I think it was a very healthy experience. I think everyone could benefit from trying to do that with their work.“

Tim Wang, 2018 Category Winner

“I think it’s really remarkable to have a prize for young researchers because most of the prizes reward people that are established in their fields. And for us, it means a great deal, because we are only launching our careers now, and such a prize is probably going to a be an extreme help.”

Mijo Simunovic, 2017 Category Winner

APPLY NOW

Flu Attack! How A Virus Invades Your Body

Thu, 22 Aug 2013 08:09:51 -0500

When you get the flu, viruses turn your cells into tiny factories that help spread the disease. In this animation, NPR's Robert Krulwich and medical animator David Bolinsky explain how a flu virus can trick a single cell into making a million more viruses. See and hear the rest of the story on NPR.org: http://www.npr.org/templates/story/story.php?storyId=114075029 Credit: Robert Krulwich, David Bolinsky, Jason Orfanon

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

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