BOL: Related items

Bourque Lab

Mon, 14 Jan 2019 15:39:25 -0600

The goal of the lab is to understand mammalian genomes using comparative genomic and epigenomic analyses. Areas of interest include: the evolution of regulatory sequences, the role of transposable elements in gene regulation and the impact of genome rearrangements in evolution and cancer.

As a computational genomicists our work involves examining billions of DNA base pairs and interpreting how variation impacts basic biology and disease. We develop computational methods and resources for the functional annotation of genomes with a special emphasis on sequencing-based assays (e.g. ChIP-seq, RNA-Seq, exome- and whole-genome sequencing, single-cell analysis).

http://www.computationalgenomics.ca

gget

BioStar — Sat, 01 Apr 2023 09:42:07 -0500

gget is a free, open-source command-line tool and Python package that enables efficient querying of genomic databases. gget consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying in a single line of code.

Address of the bookmark: https://github.com/pachterlab/gget

Figeno: Tool for plotting sequencing data along genomic coordinates.

LEGE — Tue, 17 Sep 2024 02:28:15 -0500

Tool for plotting sequencing data along genomic coordinates.

FIGENO is a
  FIGure
    GENerator
for GENOmics

With figeno, you can plot various types of sequencing data along genomic coordinates. Video overview: https://www.youtube.com/watch?v=h1cBeXoSYTA.

Address of the bookmark: https://github.com/CompEpigen/figeno

DarkHorse: a method for genome-wide prediction of horizontal gene transfer

Jit — Thu, 22 Jun 2017 07:58:35 -0500

A new approach to rapid, genome-wide identification and ranking of horizontal transfer candidate proteins is presented. The method is quantitative, reproducible, and computationally undemanding. It can be combined with genomic signature and/or phylogenetic tree-building procedures to improve accuracy and efficiency. The method is also useful for retrospective assessments of horizontal transfer prediction reliability, recognizing orthologous sequences that may have been previously overlooked or unavailable. These features are demonstrated in bacterial, archaeal, and eukaryotic examples.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852411/

ShadowCaster: a hybrid approach for the detection of horizontal gene transfer events in prokaryotes

Jit — Tue, 14 Jul 2020 06:42:10 -0500

ShadowCaster implements an evolutionary model to calculate Bayesian likelihoods for each ‘alien genes’ with an unusual sequence composition according to the host genome background to detect HGT events in prokaryotes.

https://www.mdpi.com/2073-4425/11/7/756/htm

https://shadowcaster.readthedocs.io/en/latest/

https://github.com/dani2s/ShadowCaster_testData

Address of the bookmark: https://github.com/dani2s/ShadowCaster

The Human Genome Project Video 3D Animation Introduction Low)

Sat, 24 Aug 2013 19:01:19 -0500

LAPTI Lab

Thu, 12 Dec 2013 18:19:12 -0600

The main theme of our research is the understanding of how genetic information is decoded from DNA into RNA and proteins. Someone may find this topic a little strange and argue that we already know how this is happening.

Translational recoding.

RNA editing.

Evolution of the genetic code and translation.

More at http://lapti.ucc.ie/research.html

Lab page http://lapti.ucc.ie/index.html

Chekulaevalab

Tue, 12 Jan 2016 02:32:03 -0600

Focusing on understanding the molecular mechanisms that regulate mRNA translation, localization and stability and role of non-coding RNAs in this process. Up to 90% of human DNA is estimated to be transcribed into so called non-coding RNAs that are not translated into proteins. Many of them act as potent modifiers of gene expression. miRNAs are a class of such short non-coding RNAs. They regulate expression of more than a half of eukaryotic genes, thus, affecting multiple biological processes, including cell proliferation, differentiation, apoptosis and senescence. Not surprisingly, miRNAs are involved in many human pathologies, including cancer and neurological disorders and hold great potential as drug targets, disease markers, as well as therapeutic agents.
Our lab is located at the Berlin Institute for Medical Systems Biology (BIMSB), a part of the Max Delbrück Center for Molecular Medicine (MDC).

http://www.chekulaevalab.org/

iRNAD: a computational tool for identifying D modification sites in RNA sequence

Abhimanyu Singh — Thu, 16 May 2019 00:20:07 -0500

iRNAD, for identifying D modification sites in RNA sequence. In this predictor, the RNA samples derived from five species were encoded by nucleotide chemical property and nucleotide density. Support vector machine was utilized to perform the classification.

http://lin-group.cn/server/iRNAD/

Address of the bookmark: http://lin-group.cn/server/iRNAD/

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/