BOL: Related items

Type of SSR

BioStar — Thu, 09 Mar 2023 04:35:41 -0600

Types of SSRs (simple sequence repeats), SSRs are short DNA sequences consisting of a tandem repeat of a few nucleotides, typically 2-6 nucleotides in length. There are different types of SSRs based on the length and pattern of the repeated sequence, as well as the presence or absence of interruptions of non-repeated nucleotides within the repeat array. The four types of SSRs are:

Perfect SSR: This is the simplest type of SSR, where the same repeat motif is present adjacent to each other without any interruption of any other nucleotide. For example, a perfect SSR with the repeat motif "CAT" would be "CATCATCATCAT", where the "CAT" sequence is repeated four times.
Imperfect SSR: This type of SSR contains repeat motifs that are interrupted by one or a few non-repeat nucleotides. For example, an imperfect SSR with the repeat motif "CAT" would be "CATCATGGCATCATCAT", where the "CAT" sequence is repeated twice, but interrupted by "GG".
Compound perfect SSR: This type of SSR contains two or more repeat motifs lying adjacent to each other, separated by no or very few intervening nucleotides. For example, a compound perfect SSR with the repeat motifs "CAT" and "GTC" would be "CATCATCATGTCGTC", where the "CAT" sequence is repeated three times, followed by the "GTC" sequence repeated twice.
Compound imperfect SSR: This type of SSR contains two or more repeat motifs interrupted by several non-repeat nucleotides. For example, a compound imperfect SSR with the repeat motifs "CAT" and "GTC" would be "CATCATCATNNNNNNNGTCGTCGTC", where the "CAT" sequence is repeated three times, interrupted by several non-repeat nucleotides, followed by the "GTC" sequence repeated three times.

Stephen Friend: The hunt for "unexpected genetic heroes"

Sat, 31 May 2014 14:31:47 -0500

What can we learn from people with the genetics to get sick — who don't? With most inherited diseases, only some family members will develop the disease, while others who carry the same genetic risks dodge it. Stephen Friend suggests we start studying those family members who stay healthy. Hear about the Resilience Project, a massive effort to collect genetic materials that may help decode inherited disorders. TEDTalks is a daily video podcast of the best talks and performances from the TED Conference, where the world's leading thinkers and doers give the talk of their lives in 18 minutes (or less). Look for talks on Technology, Entertainment and Design -- plus science, business, global issues, the arts and much more. Find closed captions and translated subtitles in many languages at http://www.ted.com/translate Follow TED news on Twitter: http://www.twitter.com/tednews Like TED on Facebook: https://www.facebook.com/TED Subscribe to our channel: http://www.youtube.com/user/TEDtalksDirector

YAMP: Yet Another Metagenomic Pipeline

BioStar — Sat, 06 Jul 2024 04:26:00 -0500

YAMP is constructed on Nextflow, a framework based on the dataflow programming model, which allows writing workflows that are highly parallel, easily portable (including on distributed systems), and very flexible and customisable, characteristics which have been inherited by YAMP. New modules can be added easily and the existing ones can be customised -- even though we have already provided default parameters deriving from our own experience.

Address of the bookmark: https://github.com/alesssia/YAMP

INSPIRE Faculty Scheme: a component of “Assured Opportunity for Research Career (AORC)” under INSPIRE.

Sat, 19 Jul 2014 14:59:30 -0500

Ministry of Science and Technology, Department of Science and Technology

7th ADVERTISEMENT – 2014 (2)

INSPIRE Faculty Scheme: a component of “Assured Opportunity for Research Career (AORC)” under INSPIRE.

The Department of Science and Technology, Government of India, has launched the “Innovation in Science Pursuit for Inspired Research (INSPIRE)” [http://www.inspire-dst.gov.in] program in 2008.

The program aims to attract talent for study of science and careers with research. INSPIRE includes many components. The importance of Assured Career Opportunity in R&D sector has been recognized.

INSPIRE Faculty Scheme opens up an “Assured Opportunity for Research Career (AORC)” for young researchers in the age group of 27-32 years. It offers a contractual research awards to young achievers and opportunity for independent research in the near term and emerge as a future leader in the long term.

Eligibility

Essential Indian citizens and people of Indian origin including NRI/PIO status with PhD (in science, mathematics, engineering, pharmacy, medicine, and agriculture related subjects) from any recognized university in the world,

Those who have submitted their PhD Theses and are awaiting award of the degree are also
eligible. However, the award will be conveyed only after confirmation of the awarding the
PhD degree.

The upper age limit as on 1st July 2014 should be 32 years for considering support for a
period of 5 years. However, for SC and ST candidates, upper age limit will be 35 years.

Publication(s) in highly reputed Journals demonstrating research potential of the candidate.

Desirable

Candidates who are within top 1% at the School Leaving Examination, IIT-JEE rank, 1st Rank Holder either in graduation or post-graduation level university examination (which are used presently for identifying INSPIRE Scholars at under-graduate level and INSPIRE Fellows for doctoral degree)

More at http://www.inspire-dst.gov.in/faculty_scheme.html

Does anyone have Nanopore latest updates?

Poonam Mahapatra — Mon, 12 Aug 2013 12:19:29 -0500

There was a lot of buzz about Oxford Nanopore Technologies® is developing the GridION™ system and miniaturised MinION™ device. These are a new generation of electronic molecular analysis system for use in scientific research, personalised medicine, crop science, security/defence and more. The platform technology uses nanopores to analyse single molecules including DNA/RNA and proteins. With a broad patent portfolio, the Oxford Nanopore pipeline includes biological nanopores and solid-state nanopores.

Is this available, or still under trial mode?

https://www.nanoporetech.com/

https://www.nanoporetech.com/technology/the-minion-device-a-miniaturised-sensing-system/the-minion-device-a-miniaturised-sensing-system

A powerful, yet simple, gene set analysis tool for interpreting RNA-seq and NGS results.

Shani — Thu, 30 Oct 2014 09:19:29 -0500

LifeMap Sciences is introducing GeneAnalytics, our new gene set analysis tool, which is applicable for NGS results and differentially expressed gene lists from variable sources. GeneAnalytics provides gene associations with tissues & cells, diseases, pathways, GO terms and compounds.

Our main advantages over other similar tools are:

GeneAnalytics is very simple and intuitive to use.
GeneAnalytics is based on our proprietary databases – GeneCards, MalaCards, PathCards and LifeMap Discovery, each of them integrates information from a very large number of resources.
GeneAnalytics supplies links for extensive background information on each of the matched results.

I invite you to try it out for free at geneanalytics.genecards.org, and would be happy to hear your comments and thoughts on how we can improve.

Yours,

Shani Ben-Ari Fuchs

LifeMap Sciences Team

NCBI Webinar

Jit — Sun, 08 Jun 2014 02:47:01 -0500

In less than two weeks, NCBI will offer a webinar entitled "Introducing 3 NCBI Resources to Navigate Testing for Disease Linked Variants: MedGen, GTR and ClinVar". This webinar will delve into the lifecycle of genetic testing and teach attendees how to navigate the NIH Genetic Testing Registry, ClinVar, and MedGen resources. These resources can be used to prepare for clinical cases, access detailed information about orderable genetic tests, interpret test results, and more.

More at https://attendee.gotowebinar.com/register/8452228815737989634

karyoploteR: plot whole genomes with arbitrary data

Abhimanyu Singh — Fri, 02 Feb 2018 03:24:28 -0600

karyoploteR is an R package to create karyoplots, that is, representations of whole genomes with arbitrary data plotted on them. It is inspired by the R base graphics system and does not depend on other graphics packages. The aim of karyoploteR is to offer the user an easy way to plot data along the genome to get broad genome-wide view to facilitate the identification of genome wide relations and distributions.

Address of the bookmark: https://bernatgel.github.io/karyoploter_tutorial/

Internship program with ArrayGen Technolgies

Sun, 22 Jun 2014 23:18:31 -0500

Internship Program for Bioinformatics / Biotechnology Professionals Currently we offer positions to outstanding students interested in Next Generation Sequencing (NGS) data analysis. Applications are accepted throughout the year. Accepted students will be listed on web with their schedules. Accepted students can attend our future workshops and trainings freely at the specified venue.

Interested candidates may email their resume along with a cover letter to careers@arraygen.com

Official website: http://www.arraygen.com/

GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.

Abhimanyu Singh — Tue, 23 May 2017 05:20:32 -0500

GRASS (GeneRic ASsembly Scaffolder)-a novel algorithm for scaffolding second-generation sequencing assemblies capable of using diverse information sources. GRASS offers a mixed-integer programming formulation of the contig scaffolding problem, which combines contig order, distance and orientation in a single optimization objective. The resulting optimization problem is solved using an expectation-maximization procedure and an unconstrained binary quadratic programming approximation of the original problem. We compared GRASS with existing HTS scaffolders using Illumina paired reads of three bacterial genomes. Our algorithm constructs a comparable number of scaffolds, but makes fewer errors. This result is further improved when additional data, in the form of related genome sequences, are used.

Address of the bookmark: https://github.com/AlexeyG/GRASS