ORFfinder is a graphical analysis tool for finding open reading frames (ORFs). We’ve been working on a few updates, and we’d like to find out what you think about them. Read on to find out what you can do with the new ORFfinder.

Smart BLAST (https://ncbiinsights.ncbi.nlm.nih.gov/2015/07/29/smartblast/)

Select one or a group of ORFs and BLAST several databases at once, and use the newly developed SmartBLAST to verify protein names. Looking for the traditional results from BLAST? They’re there too.

• optimized to work with vast amount of data and very large file sets (~ 10,000 - 100,000).
• allows the selective retrieval of only the required files (file masks, ls-lR parsing, recursive search, updates)
• has a built-in repository containing the settings for the most common bioinformatics download needs
• built-in wizard for batch post-processing of downloaded files (archive extraction, file conversion, etc.)
• capable of performing multiple download or update tasks simultaneously

BioDownloader has a built-in repository containing the settings for common bioinformatics file-synchronization needs, including the Protein Data Bank (PDB) and National Center for Biotechnology Information (NCBI) databases. It can post-process downloaded files, including archive extraction and file conversions.

http://dunbrack.fccc.edu/BioDownloader/

Address of the bookmark: http://dunbrack.fccc.edu/BioDownloader/

Magic-BLAST incorporates within the NCBI BLAST code framework ideas developed in the NCBI Magic pipeline, in particular hit extensions by local walk and jump (http://www.ncbi.nlm.nih.gov/pubmed/26109056), and recursive clipping of mismatches near the edges of the reads, which avoids accumulating artefactual mismatches near splice sites and is needed to distinguish short indels from substitutions near the edges.

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

As mentioned before, working with BLAST+ in Docker and the cloud has several advantages:

• Docker manages installation and maintenance of the BLAST programs and databases.
• Docker makes it is easier to integrate BLAST with other tools in your pipelines.
• NCBI BLAST databases are pre-loaded now on the both the Google Cloud and Amazon Cloud, providing fast access.

You can also use the BLAST+ Docker image on any Docker-enabled platform, such as another cloud platform or on your local computer.

See the  BLAST+ in the Cloud and  database information documentation to get started.

If you have any questions, please email us at blast-help@ncbi.nlm.nih.gov

Source:Dave Arndt

What’s included in this release?

As of July 8, 2024, this full release incorporates genomic, transcript, and protein data containing:

• 448,507,905 records
• 334,845,613 proteins
• 63,542,774 RNAs
• Sequences from 152,668 organisms

The release is provided in several directories as a complete dataset and also as divided by logical groupings.

James Webb Space Telescope's Revelations: Since its launch, the James Webb Space Telescope has provided unprecedented insights into the cosmos, unveiling details about the early universe and distant galaxies that were previously beyond our reach.

Re-establishing Contact with Voyager 1: In a testament to human ingenuity, scientists successfully re-established communication with Voyager 1, the spacecraft launched in 1977 now traversing interstellar space, offering data from the far reaches of our solar system.

Advancements in Human Biology: The global cell atlas project released its initial findings, mapping human cells with unprecedented detail, akin to a "Google Maps for the body." Additionally, the first complete map of a fruit fly's brain was unveiled, promising new insights into neurological diseases.

Public Health Milestones: The rollout of the first malaria vaccines and the commencement of late-stage clinical trials for a new tuberculosis vaccine—the first in over a century—marked significant strides in combating these diseases. Efforts against HIV/AIDS also showed promising progress, particularly in Africa.

Weight-Loss Drugs' Expanded Potential: Medications initially developed for weight loss demonstrated potential in treating a range of other diseases, indicating a broader therapeutic application than previously anticipated.

Robotics and Quantum Computing: Technological advancements brought robots capable of performing more complex tasks and moved quantum computing closer to practical, real-world applications, heralding a new era in computing and automation.

Synthetic Biology Concerns: Leading researchers, including Nobel laureates, raised alarms about the potential risks associated with synthetic biology, particularly the creation of "mirror bacteria," underscoring the need for careful regulation in this rapidly evolving field.

Climate Change Insights: Studies indicated that global CO₂ emissions plateaued with only a 0.1% increase in 2023, suggesting a potential turning point in emission trends. However, concerns about climate tipping points, such as the Atlantic Meridional Overturning Current, highlighted the urgency for continued action.

New Antibiotic Class Discovered: A novel class of antibiotics targeting multi-drug resistant bacteria was discovered, offering hope in the fight against antibiotic-resistant infections.

The new visrus are about one micron—a thousandth of a millimeter—in length, the newfound genus Pandoravirus dwarfs other viruses, which range in size from about 50 nanometers up to 100 nanometers. A genus is a taxonomic ranking between species and family.

Find  more at @ http://www.nature.com/scitable/blog/viruses101/newly_found_pandoraviruses_hint_at

http://news.nationalgeographic.co.uk/news/2013/07/130718-viruses-pandoraviruses-science-biology-evolution/

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

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