BOL: Related items

Reactome Pathway Database

BioStar — Mon, 31 Dec 2018 02:41:33 -0600

REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic and clinical research, genome analysis, modeling, systems biology and education. Founded in 2003, the Reactome project is led by Lincoln Stein of OICR, Peter D’Eustachio of NYULMC, Henning Hermjakob of EMBL-EBI, and Guanming Wu of OHSU.

Address of the bookmark: https://reactome.org/

New BLAST Core Nucleotide Database (core_nt)

LEGE — Tue, 13 Aug 2024 07:12:53 -0500

The Core Nucleotide Database (core_nt) is now the default nucleotide BLAST database. Core_nt is also available on the command line. You get faster searches & more focused results.

Core_nt contains the same eukaryotic transcript and gene-related sequences as nt. The core_nt database is nt without most eukaryotic chromosome sequences. Most nucleotide BLAST searches with core_nt will be similar to the nt database. However, core_nt is better than nt for accomplishing your most common BLAST search goals, such as identifying gene-related sequences like transcript sequences and complete bacterial chromosomes. This is because, in recent years, nt has acquired more low-relevance, non-annotated, and non-gene content.

Learn more: https://ncbiinsights.ncbi.nlm.nih.gov/2024/07/18/new-blast-core-nucleotide-database/

Updated ranking of institutes and countries based on developed biological databases

Rahul Nayak — Fri, 11 Jan 2019 09:35:26 -0600

Updated ranking of institutes and countries based on developed biological databases is available at https://lnkd.in/fiVAdM6 , India is maintaing 4th position and "Institute of Microbial Technology, Chandigarh" is on 3rd Position (after EBI and NCBI). This is a big achievement for any institute to reach on 3rd position in the world.

More at http://bigd.big.ac.cn/databasecommons/stat

DEG 5.0: a database of essential genes in both prokaryotes and eukaryotes

Rahul Nayak — Tue, 30 Mar 2021 11:47:28 -0500

Essential genes are those indispensable for the survival of an organism, and their functions are therefore considered a foundation of life. Determination of a minimal gene set needed to sustain a life form, a fundamental question in biology, plays a key role in the emerging field, synthetic biology.

DEG is freely available at the website http://tubic.tju.edu.cn/deg or http://www.essentialgene.org.

Address of the bookmark: http://www.essentialgene.org/

ChIPBase: open database for studying the transcription factor binding sites and motifs

Abhi — Wed, 29 Dec 2021 05:36:03 -0600

ChIPBase v2.0 is an open database for studying the transcription factor binding sites and motifs, and decoding the transcriptional regulatory networks of lncRNAs, miRNAs, other ncRNAs and protein-coding genes from ChIP-seq data. Our database currently contains ~10,200 curated peak datasets derived from ChIP-seq methods in 10 species.

Address of the bookmark: https://rna.sysu.edu.cn/chipbase/

Cancer's origins revealed

Jitendra Narayan — Thu, 15 Aug 2013 13:06:56 -0500

Researchers have provided the first comprehensive compendium of mutational processes that drive tumour development. Together, these mutational processes explain most mutations found in 30 of the most common cancer types. This new understanding of cancer development could help to treat and prevent a wide-range of cancers.

More at >> http://www.sanger.ac.uk/about/press/2013/130814.html

The Human Genome Project Video 3D Animation Introduction Low)

Sat, 24 Aug 2013 19:01:19 -0500

How DNA is Packaged (Advanced)

Mon, 23 Sep 2013 18:08:34 -0500

Each chromosome consists of one continuous thread-like molecule of DNA coiled tightly around proteins, and contains a portion of the 6,400,000,000 basepairs (DNA building blocks) that make up your DNA. Originally created for DNA Interactive ( http://www.dnai.org ). TRANSCRIPT: In this animation we'll see the remarkable way our DNA is tightly packed up to fit into the nucleus of every cell. The process starts with assembly of a nucleosome, which is formed when eight separate histone protein subunits attach to the DNA molecule. The combined tight loop of DNA and protein is the nucleosome. Six nucleosomes are coiled together and these then stack on top of each other. The end result is a fiber of packed nucleosomes known as chromatin. This structure, is then looped and further packaged using other proteins (which are not shown here) to give the final "chromosomal" shapes. It is this remarkable multiple folding which allows six feet of DNA to fit into the nucleus of each cell in our body. And a typical cell nucleus is so small that ten thousand could fit on the tip of a needle. It is important to realize that chromosomes are not always present, they form only when cells are dividing. At other times, as we can see here at the end of cell division, our DNA becomes less highly organized.)

Nucl2Vec: Local alignment of DNA sequences using Distributed Vector Representation

Jit — Tue, 16 Mar 2021 05:45:44 -0500

We demonstrate a novel approach forlocal alignment of DNA reads with respect to reference genome.For this process we have used Skip-gram model for creatingencoding(Nucl2Vec) and k-nearest neighbor for the alignment.With our new approach we have reduced computation cost forlocal alignment , while achieving accuracy comparable to existingdefacto standard BWA-MEM tool.

https://prakharg24.github.io/papers/401851.full.pdf

Address of the bookmark: https://prakharg24.github.io/papers/401851.full.pdf

DNA Transcription (Advanced)

Thu, 29 Jan 2015 05:31:42 -0600

Transcription is the process by which the information in DNA is copied into messenger RNA (mRNA) for protein production. Originally created for DNA Interactive ( http://www.dnai.org ). TRANSCRIPT: The Central Dogma of Molecular Biology: "DNA makes RNA makes protein" Here the process begins. Transcription factors assemble at a specific promoter region along the DNA. The length of DNA following the promoter is a gene and it contains the recipe for a protein. A mediator protein complex arrives carrying the enzyme RNA polymerase. It manoeuvres the RNA polymerase into place... inserting it with the help of other factors between the strands of the DNA double helix. The assembled collection of all these factors is referred to as the transcription initiation complex... and now it is ready to be activated. The initiation complex requires contact with activator proteins, which bind to specific sequences of DNA known as enhancer regions. These regions may be thousands of base pairs distant from the start of the gene. Contact between the activator proteins and the initiation-complex releases the copying mechanism. The RNA polymerase unzips a small portion of the DNA helix exposing the bases on each strand. Only one of the strands is copied. It acts as a template for the synthesis of an RNA molecule which is assembled one sub-unit at a time by matching the DNA letter code on the template strand. The sub-units can be seen here entering the enzyme through its intake hole and they are joined together to form the long messenger RNA chain snaking out of the top.