BOL: Related items

RopeBWT2: Incremental construction of FM-index for DNA sequences

Rahul Nayak — Thu, 25 Oct 2018 04:48:54 -0500

RopeBWT2 is an tool for constructing the FM-index for a collection of DNA sequences. It works by incrementally inserting one or multiple sequences into an existing pseudo-BWT position by position, starting from the end of the sequences. This algorithm can be largely considered a mixture of BCR and dynamic FM-index. Nonetheless, ropeBWT2 is unique in that it may implicitlysort the input into reverse lexicographical order (RLO) or reverse-complement lexicographical order (RCLO) while building the index.

Address of the bookmark: https://github.com/lh3/ropebwt2

DeepVariant : an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Jit — Sat, 25 Jan 2020 13:28:09 -0600

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant relies on Nucleus, a library of Python and C++ code for reading and writing data in common genomics file formats (like SAM and VCF) designed for painless integration with the TensorFlow machine learning framework.

https://ai.googleblog.com/2017/12/deepvariant-highly-accurate-genomes.html

https://www.biorxiv.org/content/10.1101/092890v6

Address of the bookmark: https://github.com/google/deepvariant

HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures

Poonam Mahapatra — Thu, 04 Jun 2020 23:19:07 -0500

The HNADOCK server is to predict the binding complex structure between two nucleic acid molecules through a hierarchical docking algorihtm of an FFT-based global search strategy and an intrinsic scoring function for nucleic acid interactions. Users are required to provide the three-dimensional (3D) structures of the two molecules to be docked.

Address of the bookmark: http://huanglab.phys.hust.edu.cn/hnadock/

Common methods to discover tandem repeats

BioStar — Thu, 09 Mar 2023 02:40:52 -0600

Tandem repeats are DNA sequences that are repeated in a contiguous manner in the genome. These sequences are often used as genetic markers and are important in many areas of genetics and genomics research. Here are some methods for discovering tandem repeats in genomes:

Tandem Repeat Finder: Tandem Repeat Finder is a software tool that identifies tandem repeats in DNA sequences. It is available for free download and can be used on both nucleotide and protein sequences. The tool uses a statistical algorithm to identify repeats based on their length, copy number, and overall composition.
RepeatMasker: RepeatMasker is another software tool that can identify tandem repeats in DNA sequences. It works by comparing the input sequence to a database of known repeats and then identifies any tandem repeats that match those in the database.
PCR-based methods: Polymerase chain reaction (PCR) can be used to amplify and detect tandem repeats in genomic DNA. PCR primers are designed to flank the tandem repeat region, and amplification of the target DNA fragment can be visualized on a gel. This method can be useful for detecting novel tandem repeats and for genotyping.
Southern blotting: Southern blotting is a classic method for detecting DNA fragments in a sample. It can be used to detect tandem repeats by digesting genomic DNA with a restriction enzyme, separating the fragments by gel electrophoresis, and then probing the blot with a tandem repeat-specific probe.

Overall, a combination of these methods can be used to comprehensively identify tandem repeats in genomes.

Basics of BLAST Programs !

BioStar — Fri, 26 Jul 2024 06:04:26 -0500

The Basic Local Alignment Search Tool (BLAST) is a powerful bioinformatics program used to compare an input sequence (such as DNA, RNA, or protein sequences) against a database of sequences to find regions of similarity. Developed by the National Center for Biotechnology Information (NCBI), BLAST is widely used for identifying species, finding functional and evolutionary relationships between sequences, and predicting the function of novel sequences.

Key Features of BLAST:
1. Sequence Comparison: BLAST searches for local alignments between the query sequence and sequences in a database. It identifies regions of similarity, which can help infer functional and evolutionary relationships.

2. Speed and Efficiency: BLAST uses heuristic algorithms, making it faster than exhaustive search methods, suitable for large-scale database searches.

3. Versatility: There are several versions of BLAST for different types of sequence comparisons:
- blastn: Compares a nucleotide query sequence against a nucleotide sequence database.
- blastp: Compares a protein query sequence against a protein sequence database.
- blastx: Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.
- tblastn: Compares a protein query sequence against a nucleotide sequence database translated in all reading frames.
- tblastx: Compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.

4. Scoring and E-value: BLAST results are scored based on the quality and length of the alignments. The E-value (expect value) indicates the number of alignments one can expect to find by chance, with lower E-values representing more significant matches.

5. Output Formats: BLAST provides results in various formats, including plain text, HTML, XML, and JSON, making it adaptable for different types of analyses and integrations with other tools.

Applications of BLAST:
- Genomic Research: Identifying genes, understanding genetic diversity, and mapping genome sequences.
- Protein Function Prediction: Inferring the function of unknown proteins by comparing them to known protein sequences.
- Evolutionary Studies: Exploring evolutionary relationships between organisms by comparing their genetic material.
- Medical Research: Identifying pathogens, understanding disease mechanisms, and developing treatments by comparing sequences of interest.

Overall, BLAST is an essential tool in bioinformatics, offering a reliable and efficient way to analyze and interpret biological sequence data.

Biological databases !

BioStar — Wed, 12 Feb 2020 01:16:29 -0600

Now a days there are a lots of genomics databases available around the world. This bookmark is created to provide all links in one place ...

ftp://ftp.ncbi.nih.gov/genomes/

https://hgdownload.soe.ucsc.edu/downloads.html

Address of the bookmark: ftp://ftp.ncbi.nih.gov/genomes/

DNA tale of 3 to 4 years old Serbia boy

Rahul Agarwal — Tue, 26 Nov 2013 17:34:00 -0600

The genome of a young boy found underground at Mal’ta near Lake Baikal of eastern Siberia around 24,000 years ago came out as close relative of Europeans and Native Indians.

Link:

http://www.nytimes.com/2013/11/21/science/two-surprises-in-dna-of-boy-found-buried-in-siberia.html?_r=0

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12736.html

Bionics, Transhumanism, and the end of Evolution (Full Documentary)

Fri, 27 Sep 2013 11:54:17 -0500

Bionics, Transhumanism, and the end of Evolution (Full Documentary) . 2013 This documentary and the rest of the documentaries presented relate to important times and figures in history, historic places and sites, archaeology, science, conspiracy theories, and education. The Topics of these video documentaries are varied and cover ancient history, Rome, Greece, Egypt, science, technology, nature, planet earth, the solar system, the universe, World wars, Battles, education, Biographies, television, archaeology, Illuminati, Area 51, serial killers, paranormal, supernatural, cults, government cover-ups, corruption, martial arts, space, aliens, ufos, conspiracy theories, Annunaki, Nibiru, Nephilim, satanic rituals, religion, strange phenomenon, origins of Mankind

The Cat: evolution, domestication and Genome 10k

Sun, 10 Nov 2013 14:33:56 -0600

A public lecture by Dr Stephen J O'Brien at the UCD Earth Institute, University College Dublin, Ireland. Dr O'Brien is a world leading molecular biologist and dedicated conservationist who uses the tools of molecular biology to help protect endangered species and understand devastating diseases such as cancer and AIDS. He received his PhD in Genetics from Cornell University, USA, in 1971. He then joined the prestigious National Cancer Institute, National Institutes of Health as a post-doc in 1971 and, there, served as Founder and Chief of the Laboratory of Genomic Diversity from 1986-2011. In December 2011, he joined the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Russia, as Chief Scientific Officer. Convinced of the utility of exploring diverse species to advance our understanding of the human genome, Dr O'Brien and his team have assembled over 62,000 animal and 424,000 human tissue/DNA specimens, facilitating wide-ranging studies of disease gene associations, species adaptation and natural history. His research interests and expertise span human and comparative genomics, genetic epidemiology, HIV/AIDS, retro-virology, bioinformatics biodiversity and species conservation. Dr O'Brien is best known for documenting the remarkable genetic uniformity of African cheetahs, resolving the mammalian tree of life, describing heretofore unrecognized species of Orangutans, African forest elephants, and Bornean clouded leopards. He is credited with the discovery of CCR5 delta 32, the first of 20 human AIDS restriction genes, which imparts natural immunity to HIV. He is the one of the founders of the Genome 10K initiative, has published over 750 leading research papers, written multiple books and is adjunct professor in over 12 international leading universities. The UCD Earth Institute, University College Dublin, is a multidisciplinary research and education centre with a focus on creating and sharing new knowledge. We aim to contribute to sustainable solutions for many of the pressing Earth-related problems affecting societies now and in the near future.

The Minerva Research Group for Bioinformatics

Tue, 27 May 2014 15:48:14 -0500

The focus of the bioinformatics group is to use computational approaches to gain an insight into genome evolution in primates.

http://www.eva.mpg.de/genetics/bioinformatics/overview.html?Fsize=0%2C%20%40%2F%27

Kelso Group
Department of Evolutionary Genetics
Max Planck Institute for Evolutionary Anthropology
Deutscher Platz 6
04103 Leipzig
Germany
Phone: +49 341 3550 500

Job:
http://www.eva.mpg.de/genetics/bioinformatics/jobs.html?Fsize=0%2C%2B%40