if you map reads to GRCh38 or hg38, use the following:

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz

There are several other versions of GRCh37/GRCh38. What’s wrong with them? Here are a collection of potential issues:

More at http://lh3.github.io/2017/11/13/which-human-reference-genome-to-use

Address of the bookmark: http://lh3.github.io/2017/11/13/which-human-reference-genome-to-use

Address of the bookmark: https://doc-openbio.readthedocs.io/projects/seqmule/en/latest/

Following are the weblink for different available browsers:

http://www.ensembl.org/index.html

http://ensemblgenomes.org/

http://genome.ucsc.edu/

http://www.ncbi.nlm.nih.gov/genome

http://www.ebi.ac.uk/genomes/

http://flybase.org/

http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi

http://www.sanger.ac.uk/resources/databases/

To use CLgenomics, individual genome data (genome sequences + annotation details) are compiled and saved in a specially formatted file called CLG (ChunLab Genomics). Each CLG file corresponds with one bacterial genome. If multiple genomes are being considered and compared, multiple CLG files are needed. ChunLab offers >40,000 CLG files of publicly available Bacterial and Archaeal genomes.

Address of the bookmark: https://chunlab.wordpress.com/clgenomics-software/

Address of the bookmark: https://www.kegg.jp/kegg/tool/map_pathway.html

Address of the bookmark: https://proksee.ca/

It looks simple, but inside its microscopic body is a huge library of DNA. Most of this DNA has been passed down from its parents. But sometimes, bacteria can pick up new pieces of DNA from other bacteria.

These new pieces can give them useful abilities — such as surviving antibiotics, causing disease, or adapting to a new environment.

Scientists call some of these special DNA regions genomic islands.

But there is a problem: How do we find these hidden islands?

That is where GIPSy2 comes in.

Researchers developed GIPSy2, a computer tool that acts like a detective. It scans bacterial DNA and looks for unusual patterns that might show where a genomic island is hiding.

Instead of looking at just one clue, GIPSy2 uses several methods to investigate the DNA. It can also study many bacterial genomes, making it useful when researchers have large amounts of genetic data.

In their study, the researchers tested GIPSy2 on different bacteria. The tool was able to identify genomic regions connected with important features such as antibiotic resistance, disease-causing abilities, metabolism, and relationships with other organisms.

Think of it like searching for hidden islands on a huge map. The DNA is the ocean, and genomic islands are the small pieces of land that may contain valuable information.

GIPSy2 does not give scientists the final answer by itself. Its predictions still need to be carefully checked and, when possible, confirmed through experiments.

But it gives researchers a faster way to explore bacterial genomes and discover clues about how bacteria change and survive.

And that is why this small piece of software could help scientists better understand the invisible world of bacteria — one hidden genomic island at a time.

GIPSy2 is currently available on Zenodo repository at https://zenodo.org/doi/10.5281/zenodo.10222587

https://fhs.mcmaster.ca/gupta-lab/index.html

"In neuroscience, the project will use neuroinformatics and brain simulation to collect and integrate experimental data, identifying and filling gaps in our knowledge, and prioritising future experiments.

In medicine, the HBP will use medical informatics to identify biological signatures of brain disease, allowing diagnosis at an early stage, before the disease has done irreversible damage, and enabling personalized treatment, adapted to the needs of individual patients. Better diagnosis, combined with disease and drug simulation, will accelerate the discovery of new treatments, drastically lowering the cost of drug discovery.

In computing, new techniques of interactive supercomputing, driven by the needs of brain simulation, will impact a vast range of industries. Devices and systems, modelled after the brain, will overcome fundamental limits on the energy-efficiency, reliability and programmability of current technologies, clearing the road for systems with brain-like intelligence."

Source: http://www.forbes.com/sites/jenniferhicks/2013/10/07/the-human-brain-project-begins/ 

(https://www.facebook.com/humanbrainproj/info)

Home Page:

https://www.humanbrainproject.eu/

Jobs:

https://www.humanbrainproject.eu/participate/jobs

1. P.Pollastro, S.Rampone (2002). HS3D, a Dataset of Homo Sapiens Splice Regions, and its Extraction Procedure from a Major Public Database , International Journal of Modern Physics C, 13(8), 1105-1117. (please cite this paper)

2. P.Pollastro, S.Rampone (2003). HS3D: Homo Sapiens Splice Site Data Set , Nucleic Acids Research, 2003 Annual Database Issue.

Address of the bookmark: http://www.sci.unisannio.it/docenti/rampone/