BOL: Related items

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

BFC: a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data

Jit — Thu, 31 May 2018 09:35:23 -0500

BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes. The BFC algorithm is a variant of the classical spectrum alignment algorithm introduced by Pevzner et al (2001). It uses an exhaustive search to find a k-mer path through a read that minimizes a heuristic objective function jointly considering penalties on correction, quality and k-mer support. This algorithm was first implemented in my fermi assembler and then refined a few times in fermi, fermi2 and now in BFC. In the k-mer counting phase, BFC uses a blocked bloom filter to filter out most singleton k-mers and keeps the rest in a hash table (Melsted and Pritchard, 2011). The use of bloom filter is how BFC is named, though other correctors such as Lighter and Bless actually rely more on bloom filter than BFC. https://github.com/lh3/bfc

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

Phylogenetics

Fri, 23 Aug 2013 03:53:43 -0500

006 - Phylogenetics Paul Andersen discusses the specifics of phylogenetics. The evolutionary relationships of organisms are discovered through both morphological and molecular data. A specific type of phylogenetic tree, the cladogram, is also covered. Intro Music Atribution Title: I4dsong_loop_main.wav Artist: CosmicD Link to sound: http://www.freesound.org/people/CosmicD/sounds/72556/ Creative Commons Atribution License

A-allele of SLC24A5 gene is found to be responsible for variation in skin color of South-East Asians and Europeans

Rahul Agarwal — Tue, 12 Nov 2013 21:02:27 -0600

Key finding:

rs1426654 SNP of SLC24A5 gene is decider of skin pigmentation variation in South Asia
rs1426654-A allele is widely spread throughout the Indian subcontinent
Skin pigmentation is also account by the combination of processes like selection and demographic history of populations affected by their language and origin
Sign of positive selection in Europeans, Middle East, Pakistan, Central Asia and North India but not in South India
In European , A-allele is almost reached to fixation

Paper:

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003912

simNGS and simLibrary – Software for Simulating Next-Gen Sequencing Data

Jit — Tue, 28 Nov 2017 06:49:11 -0600

simNGS is software for simulating observations from Illumina sequencing machines using the statistical models behind the AYB base-calling software. By default, observations only incorporate noise due to sequencing and do not incorporate effects from more esoteric sources of noise that may be present in real data ("dust", bubbles, merged clusters, sequence-heterogeneous clusters, etc). Many of these additional sources may optionally applied.

simNGS takes fasta format sequences and a file describing the covariance of noise between bases and cycles observed in an actual run of the machine, randomly generates noisy intensities representing the signals for the sequence at each cycle and calculates likelihoods for all possible base calls.

Address of the bookmark: https://www.ebi.ac.uk/goldman-srv/simNGS/

Earth BioGenome Project

Jit — Wed, 25 Apr 2018 07:48:56 -0500

The central goal of the Earth BioGenome Project is to understand the evolution and organization of life on our planet by sequencing and functionally annotating the genomes of 1.5 million known species of eukaryotes, a massive group that includes plants, animals, fungi and other organisms whose cells have a nucleus that houses their chromosomal DNA. To date, the genomes of less than 0.2 percent of eukaryotic species have been sequenced.

More at https://www.ucdavis.edu/news/earth-biogenome-project-aims-sequence-dna-all-complex-life

Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm

BioStar — Mon, 16 Mar 2020 10:09:26 -0500

Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of any size. Described by Firtina et al. (preliminary version at https://arxiv.org/pdf/1902.04341.pdf

More at https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa179/5804978?rss=1

Address of the bookmark: https://github.com/CMU-SAFARI/Apollo

Entire Human Genome Sequencing !

LEGE — Tue, 02 Apr 2024 01:19:29 -0500

Cost-effective whole human genome sequencing has revolutionized the landscape of genetic research and personalized medicine by making comprehensive genetic analysis accessible to a wider population. Through advancements in sequencing technologies, such as next-generation sequencing (NGS), costs have significantly decreased, enabling researchers and healthcare providers to analyze an individual's complete genetic makeup with greater efficiency and affordability. This has profound implications for disease diagnosis, prognosis, and treatment, as it allows for the identification of genetic predispositions and the customization of healthcare interventions based on an individual's unique genetic profile. Moreover, as the cost continues to decline, the potential for population-scale genomic studies and large-scale screening programs becomes increasingly feasible, promising to further enhance our understanding of human genetics and improve healthcare outcomes on a global scale.

Here are few companies:

https://mynucleus.com/

https://myome.com/

https://nebula.org/whole-genome-sequencing-dna-test/

Compressive Genomics

Rahul Agarwal — Sun, 11 Aug 2013 11:13:58 -0500

The key to finding a solution is to notice that most genomicsequences differ by very little. It may well be that the number of complete genome sequences being stored is increasing rapidly, but the actual amount of new data is very small. In other words, a single DNA sequence isn't particularly compressible but a set of sequences shares so much in common that the redundancy can be used to store them in a much smaller storage space. (Source:e-article from Alex Armstrong)

http://www.i-programmer.info/news/181-algorithms/4537-a-new-dna-sequence-search-compressive-genomics.html

http://en.wikipedia.org/wiki/Compression_of_Genomic_Re-Sequencing_Data

http://www.nature.com/nbt/journal/v30/n7/full/nbt.2241.html

http://bioinformatics.oxfordjournals.org/content/29/13/i283.full

http://groups.csail.mit.edu/cb/cast/

Precision Medicine

Rahul Agarwal — Sat, 24 Aug 2013 15:47:03 -0500

Coupling established clinical–pathological indexes with state-of-the-art molecular profiling to create diagnostic, prognostic, and therapeutic strategies precisely tailored to each patient's requirements — hence the term “Precision medicine”

Source:http://www.nejm.org/doi/full/10.1056/NEJMp1114866

Another video on precision medicine:

http://www.youtube.com/watch?v=Pi8W0yOXnzE

Precision Medicine basically intergrates bioinformatics, genomics , genetics, molecular biology and nanotechnology to deliver precise cure/diagnotics to a specific patient.

Examples:

The drug imatinib (Gleevec) designed to inhibit an altered enzyme produced by a fused version of two genes found in chronic myelogenous leukemia.
The breast cancer drug trastuzumab (Herceptin) works only for women whose tumors have a particular genetic profile called HER-2 positive.

E.g. source :

http://www.bionews-tx.com/news/2013/08/15/how-the-impact-of-cancer-genomics-on-precision-medicine-is-revolutionizing-cancer-treatment/

Address of the bookmark: http://www.cbsnews.com/video/watch/?id=50149783n