BOL: Related items

Tech and Bioinformatics roles at Basepaws

Wed, 18 Aug 2021 23:34:25 -0500

Basepaws is an LA-based pet genomics company, quickly growing and focused on feline and canine at-home genetic and biome tests, along with many other projects and products in the works. Thank you for taking a look!

Bioinformatics : https://www.linkedin.com/jobs/view/2681785372/

Engineer: https://www.linkedin.com/jobs/view/2681796993/

Bioinformatics tools for genome assembly !

BioStar — Mon, 24 Jul 2023 07:04:26 -0500

There are numerous genome assembly tools available, each with its strengths and weaknesses. Here is a list of some widely used genome assembly tools as of my last update in September 2021:

SPAdes: An assembler specifically designed for single-cell and multi-cell bacterial genomes, as well as small eukaryotic genomes.
ABySS: A parallelized assembler for large genomes that uses de Bruijn graphs.
Velvet: Another de Bruijn graph-based assembler optimized for short-read sequencing data.
SOAPdenovo: A de Bruijn graph-based assembler designed for short reads, widely used for assembling large and complex genomes.
MaSuRCA: A hybrid assembler that combines data from multiple sequencing technologies, such as Illumina and PacBio.
Canu: A long-read assembler optimized for PacBio and Oxford Nanopore sequencing data.
Flye: A long-read assembler suitable for bacterial and small eukaryotic genomes.
SMARTdenovo: An assembler designed for long reads, particularly suited for PacBio data.
SPAdes Long Read (SPAdesLR): An extension of SPAdes for long-read data, such as those from PacBio or Nanopore.
Minia: An assembler optimized for low memory consumption, suitable for small and medium-sized genomes.
Unicycler: A hybrid assembler that combines short and long reads for circular bacterial genome assembly.
wtdbg2: A de Bruijn graph assembler for long reads, efficient for very large genomes.
Shasta: A long-read assembler that uses the Overlap-Layout-Consensus approach, suitable for PacBio and Nanopore data.
Sparc: An assembler designed to handle noisy long reads from Nanopore sequencing.
CANA: An assembler for metagenomic data, particularly for complex and diverse microbial communities.
Ra Assembler: A metagenome assembler for long reads, designed for highly complex metagenomic samples.

Please note that the field of bioinformatics is constantly evolving, and new assembly tools may have emerged since my last update. Additionally, the performance of these tools can vary depending on the characteristics of the sequencing data and the genome being assembled. When selecting an assembly tool, consider the specific requirements of your project, the available data types, and the computational resources at your disposal. Always refer to the respective tool's documentation and publications for the most up-to-date information and recommendations.

BioKit: a set of tools dedicated to bioinformatics, data visualisation

Neel — Tue, 18 Jun 2024 02:04:39 -0500

BioKit is a set of tools dedicated to bioinformatics, data visualisation (biokit.viz), access to online biological data (e.g. UniProt, NCBI thanks to bioservices). It also contains more advanced tools related to data analysis (e.g., biokit.stats). Since R is quite common in bioinformatics, we also provide a convenient module to run R inside your Python scripts or shell (:mod:biokit.rtools module).

Address of the bookmark: https://biokit.readthedocs.io/en/latest/index.html

Memories Can Be Passed Down Through DNA

Sat, 10 May 2014 21:24:10 -0500

The premise of Assassin's Creed is the reliving of other people's memories stored inside DNA. Well scientists have found that in mice, it actually happens! Anthony is joined by special guest and our friend Tara Long from Hard Science to explain how this process works, and if it might apply to humans as well. Read More: Parental olfactory experience influences behavior and neural structure in subsequent generations http://www.nature.com/neuro/journal/vaop/ncurrent/abs/nn.3594.html "Using olfactory molecular specificity, we examined the inheritance of parental traumatic exposure, a phenomenon that has been frequently observed, but not understood." What Is Epigenetics? http://www.sciencemag.org/content/330/6004/611 "The cells in a multicellular organism have nominally identical DNA sequences (and therefore the same genetic instruction sets), yet maintain different terminal phenotypes. This nongenetic cellular memory, which records developmental and environmental cues (and alternative cell states in unicellular organisms), is the basis of epi-(above)-genetics." Epigenetics http://en.wikipedia.org/wiki/Epigenetics Watch More: How to Change Your Genes https://www.youtube.com/watch?v=B5DU9lgbsSE TestTube Wild Card http://testtube.com/dnews/dnews-231-how-too-many-screens-affect-our-brain?utm_source=YT&utm_medium=DNews&utm_campaign=DNWC Is Sexiness Hereditary? https://www.youtube.com/watch?v=z6STRCncvM8 ____________________ DNews is dedicated to satisfying your curiosity and to bringing you mind-bending stories & perspectives you won't find anywhere else! New videos twice daily. Watch More DNews on TestTube http://testtube.com/dnews Subscribe now! http://www.youtube.com/subscription_center?add_user=dnewschannel DNews on Twitter http://twitter.com/dnews Anthony Carboni on Twitter http://twitter.com/acarboni Laci Green on Twitter http://twitter.com/gogreen18 Trace Dominguez on Twitter http://twitter.com/trace501 DNews on Facebook http://facebook.com/dnews DNews on Google+ http://gplus.to/dnews Discovery News http://discoverynews.com

Programming language to build synthetic DNA

Jit — Mon, 30 Sep 2013 16:37:24 -0500

A team led by Georg Seelig (http://homes.cs.washington.edu/~seelig/index.html) at University of Washington has developed a programming language for chemistry that it hopes will streamline efforts to design a network that can guide the behavior of chemical-reaction mixtures in the same way that embedded electronic controllers guide cars, robots and other devices. In medicine, such networks could serve as “smart” drug deliverers or disease detectors at the cellular level.

Reference & More @

http://www.nature.com/nnano/journal/vaop/ncurrent/full/nnano.2013.189.html

http://www.washington.edu/news/2013/09/30/uw-engineers-invent-programming-language-to-build-synthetic-dna/

Image source: washington.edu

Research assistant in computational biology

Wed, 24 Jun 2015 07:55:16 -0500

http://www.au.dk/en/about/vacant-positions/scientific-positions/stillinger/Vacancy/show/743161/5283/

Qualifications:
MSc degree in computer science, engineering, genetics or similar field with a strong emphasis on computational methods.

Deadline
01.08.2015

A History of Bioinformatics (in the Year 2039)

Wed, 23 Jul 2014 06:37:51 -0500

C. Titus Brown http://video.open-bio.org/video/1/a-history-of-bioinformatics-in-the-year-2039

MitoFinder

Neel — Tue, 29 Aug 2023 02:13:01 -0500

Allio, R., Schomaker-Bastos, A., Romiguier, J., Prosdocimi, F., Nabholz, B., & Delsuc, F. (2020) Mol Ecol Resour. 20, 892-905. (publication link)

Mitofinder is a pipeline to assemble mitochondrial genomes and annotate mitochondrial genes from trimmed read sequencing data.

MitoFinder is also designed to find and annotate mitochondrial sequences in existing genomic assemblies (generated from Hifi/PacBio/Nanopore/Illumina sequencing data...)

MitoFinder is distributed under the license.

Address of the bookmark: https://github.com/RemiAllio/MitoFinder

LTR_Finder: an efficient program for finding full-length LTR retrotranspsons in genome sequences.

Neel — Sun, 13 Jan 2019 07:05:53 -0600

LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences.

The Program first constructs all exact match pairs by a suffix-array based algorithm and extends them to long highly similar pairs. Then Smith-Waterman algorithm is used to adjust the ends of LTR pair candidates to get alignment boundaries. These boundaries are subject to re-adjustment using supporting information of TG..CA box and TSRs and reliable LTRs are selected. Next, LTR_FINDER tries to identify PBS, PPT and RT inside LTR pairs by build-in aligning and counting modules. RT identification includes a dynamic programming to process frame shift. For other protein domains, LTR_FINDER calls ps_scan (from PROSITE, http://www.expasy.org/prosite/) to locate cores of important enzymes if they occur.

Address of the bookmark: https://github.com/xzhub/LTR_Finder

OSDDlinux : Computational resources for drug discovery

Archana Malhotra — Sun, 22 Sep 2013 13:15:58 -0500

Open Source Drug Discovery (OSDD), a mission to provide affordable drugs for poors, is in the process of creating an in silico plateform for designing, discovering and simulating drugs. OSDD have initiate number of projects to support in silico drug discovery, including OSDDlinux and computational resources for drug discovery (CRDD).

The main purpose of OSDDLinux is to provide an in silico platform for computer-aided drug design. This is a collection and compilation of large number of software and web services which will be directly or indirectly useful for researches working in the field of drug design/discovery. Overall objective of OSDDlinux is to promote open source in drug discovery, crowdsourcing and network based collobrations. Following are major features of OSDDlinux ...

Find more @ http://osddlinux.osdd.net/index.php