BOL: Related items

pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks

Neel — Fri, 09 Nov 2018 12:34:23 -0600

pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:

bigwig
bed (many options)
bedgraph
links (represented as arcs)
Hi-C matrices (if HiCExplorer is installed)

Address of the bookmark: https://github.com/deeptools/pyGenomeTracks

jtools : more efficient presentation of regression analyses

Neel — Tue, 11 Feb 2020 23:10:49 -0600

This package consists of a series of functions created by the author (Jacob) to automate otherwise tedious research tasks. At this juncture, the unifying theme is the more efficient presentation of regression analyses. There are a number of functions for other programming and statistical purposes as well. Support for the survey package’s svyglm objects as well as weighted regressions is a common theme throughout.

Notice: As of jtools version 2.0.0, all functions dealing with interactions (e.g., interact_plot(), sim_slopes(), johnson_neyman()) have been moved to a new package, aptly named interactions.

Address of the bookmark: https://cran.r-project.org/web/packages/jtools/readme/README.html

Circos visualization !

BioStar — Mon, 06 Mar 2023 06:01:32 -0600

Circos visualization

https://wlcb.oit.uci.edu/modules/index.html

Address of the bookmark: https://wlcb.oit.uci.edu/NG-Circos

Is reference genome necessary for gene expression study in transcriptome sequencing or for variant discovery in genome sequencing?

Rahul Agarwal — Wed, 17 Jul 2013 15:25:09 -0500

Like in case of plant genomes where nature of genome is too complex and huge in size to accomplish complete de novo assembly by current sequencing technology. What would be alternate solution? Can we live in reference free world?

Want to Know which genome assembler rule the world ?

Rahul Agarwal — Sun, 11 Aug 2013 11:42:32 -0500

Assemblathon 2: evaluating de novo methods of genome assembly

http://www.gigasciencejournal.com/content/2/1/10/abstract

http://blogs.nature.com/news/2013/07/genome-assembly-contest-prompts-soul-searching.html

http://assemblathon.org/post/44431915644/feedback-and-analysis-of-the-assemblathon-2-p

Barber pole worm , sheep pathogen sequenced !!!

Rahul Agarwal — Tue, 03 Sep 2013 16:32:18 -0500

Haemonchus contortus is a highly pathogenic parasitic nematode of that can infect a large number of wild and domesticated ruminant species and is the most economically important parasite of sheep and goats worldwide. Scientists at the Wellcome Trust Sanger Institute have sequenced the genome of the barber's pole worm (Haemonchus contortus), which will help to explore the this tropical parasite which been disseminated around the world by livestock movement.

H. contortus is a member of the superfamily trichostrongyloidea (Strongylida) which contains most of the economically important parasitic nematodes of grazing livestock. These parasites cost the global livestock industry billions of dollars per annum in lost production and drug costs. A common type of clover may be a preventative or palliative for the disease. However, some particular breeds of sheep, such as the Gulf Coast Native from the Southern United States, have been shown to have developed special resistance to H. contortus.

Getting the full genome can help to tackle the problem and understand the resistance mechanism with an ease. Moreover, the genome could now provide a comprehensive understanding of how treatments against parasitic worms work and point to further new treatments and vaccines. By comparing the genome of the barber's pole worm with those of worms that have acquired drug resistance, researchers expect to reveal information about how and why resistance has occurred. Till now, researchers have uncovered essential information in the fight against drug resistance in worms.

Reference:

http://www.fwi.co.uk/articles/28/08/2013/140758/researchers-close-in-on-worm-resistance-in-sheep.htm

http://www.sciencedaily.com/releases/2013/08/130828103351.htm?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+sciencedaily%2Fplants_animals+(ScienceDaily%3A+Plants+%26+Animals+News)

Image source: Wikipedia

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

Genome of Rainbow Trout Sequenced

Rahul Agarwal — Fri, 25 Apr 2014 10:36:51 -0500

Major finding:

“In humans and most vertebrates the duplication events were older so there are fewer duplicated genes still present. Most of the duplicated genes get lost or modified so much that they are no longer recognizable as duplicates over time. In the trout and salmon we can see an earlier stage in the process and many duplicated genes are still present,” said Dr Gary Thorgaard of Washington State University, a co-author of the paper published in the journal Nature Communications.

Source:

http://www.sci-news.com/genetics/science-genome-rainbow-trout-01877.html

Real time Sequencing

Rahul Agarwal — Sun, 04 May 2014 18:16:42 -0500

“... we now know we can do high-throughput sequencing at any location on Earth,” Moroz said.

Source:

http://news.ufl.edu/2014/04/28/real-time-genome-sequencing-at-sea/

miRNA database and tools

Rahul Agarwal — Mon, 09 Jun 2014 07:58:40 -0500

Since few years miRNA has shown to play important role in therapeutic related research and also known to play vital role in controlling gene expression specifically at transcriptional and post-transcription levels. Here are some important DBs and tools related with miRNA:

miRNA Sequencing data analysis : http://tools.genxpro.net/omiras/

miRNApath( R based tool) : http://www.bioconductor.org/packages/release/bioc/html/miRNApath.html

miRWalk DB : http://www.umm.uni-heidelberg.de/apps/zmf/mirwalk/

TargetScanHuman : http://www.targetscan.org/

RNAhybrid : http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/welcome.html

RNA22 predictor : http://cbcsrv.watson.ibm.com/rna22.html

miRNA predictor : http://www.microrna.org/microrna/home.do

Plant miRNA DB :http://bioinformatics.cau.edu.cn/PMRD/

miRBASE DB: http://www.mirbase.org/

Plant RNA predictor : http://plantgrn.noble.org/psRNATarget/

miRNA Interaction DB : http://starbase.sysu.edu.cn/

Sequencing based miRNA DB : http://mirgator.kobic.re.kr/

predicted A-to-I edited miRNA DB : http://microrna.osumc.edu/mireditar/

Animal, plant and virus miRNA DB : http://lemur.amu.edu.pl/share/php/mirnest/

Atlantic Salmon miRNAs DB : http://www.molgenv.com/ssa_mirnas_db_home.php

miRNA prediction on UTRs : http://genie.weizmann.ac.il/pubs/mir07/mir07_prediction.html

Idea of analysing miRNA Sequencing data :

http://www.illumina.com/applications/epigenetics/small_rna_analysis.ilmn

More:

http://www.bioconductor.org/help/search/index.html?q=miRNA+target