BOL: Related items

GenoFig: a user-friendly application for the visualization and comparison of genomic regions

BioStar — Mon, 05 Aug 2024 23:06:58 -0500

Tool for graphical vizualisation of annotated genetic regions, and homologous regions comparison. It is an independent recoding of Easyfig 2 initially developped by at the S. Beatson Lab [https://mjsull.github.io/Easyfig/]

Download the GenoFig source code using the 'Download' button on top of this page. Cloning is currently not available for people not member of the INRAE French Institution. After decompression, open a terminal in the folder containing the decompressed files and run:

conda env create -f extras/requirements.yml
extras/SETUP.sh

Address of the bookmark: https://forgemia.inra.fr/public-pgba/genofig

SIMON BOULTON LAB

Tue, 11 Dec 2018 09:01:46 -0600

DNA is quite fragile and easily damaged, both by the normal processes of life at work within our cells and by external agents such as the chemicals in tobacco smoke or ultraviolet (UV) rays from the sun. However, our cells have evolved clever ‘repair kits’ that spot DNA damage and patch it up, helping to protect us against tumours. If these repair kits are faulty or inefficient then mistakes can quickly build up and cause cells to become cancerous.

They are particularly interested in a type of DNA repair known as double-strand break repair, which happens when the DNA molecule has been completely snapped in two. Not only does this happen in normal cells in the body to repair DNA damage, but it also occurs when eggs and sperm are made (known as meiosis) and during the generation of cells in the immune system.

https://www.crick.ac.uk/research/labs/simon-boulton

Frontend: Perl Web framework documentation - Andrej Sali Lab

Jit — Mon, 08 Jan 2018 22:32:03 -0600

The frontend is a set of Perl classes that displays the web interface, allowing a user to upload their input files, start a job, display a list of all jobs in the system, and get back job results. The main saliwebfrontend class must be subclassed for each web service. This class is then used to display the web pages using a set of CGI scripts that are set up automatically by the build system.

Address of the bookmark: https://saliweb.readthedocs.io/en/latest/frontend.html

PilonGrid: parallel wrapper around the Pilon framework

Rahul Nayak — Thu, 13 Dec 2018 09:35:40 -0600

The distribution is a parallel wrapper around the Pilon framework The pipeline is composed of bash scripts, an example mapping.fofn which shows how to input your fastq files (you give paths to the R1 file), and how to launch the pipeline.

Address of the bookmark: https://github.com/skoren/PilonGrid

ALF--a simulation framework for genome evolution.

Jit — Tue, 22 Oct 2019 22:05:58 -0500

Artificial Life Framework (ALF) simulates a root genome into a number of related genomes. Result files include the resulting gene sequences, true tree and true MSAs. A description of ALF can be found in the following article:

Daniel A Dalquen, Maria Anisimova, Gaston H Gonnet, Christophe Dessimoz: ALF - A Simulation Framework for Genome Evolution. Mol Biol Evol, 29(4):1115-1123, April 2012.
http://mbe.oxfordjournals.org/content/29/4/1115

Address of the bookmark: http://alfsim.org/#index

CAR: Reconstructing Contiguous Regions of an Ancestral Genome

Abhimanyu Singh — Thu, 18 May 2017 05:24:01 -0500

We describe a new method for predicting the ancestral order and orientation of those intervals from their observed adjacencies in modern species. We combine the results from this method with data from chromosome painting experiments to produce a map of an early mammalian genome that accounts for 96.8% of the available human genome sequence data. The precision is further increased by mapping inversions as small as 31 bp. Analysis of the predicted evolutionary breakpoints in the human lineage confirms certain published observations but disagrees with others. Although only a few mammalian genomes are currently sequenced to high precision, our theoretical analyses and computer simulations indicate that our results are reasonably accurate and that they will become highly accurate in the foreseeable future. Our methods were developed as part of a project to reconstruct the genome sequence of the last ancestor of human, dogs, and most other placental mammals;

Address of the bookmark: http://www.bx.psu.edu/miller_lab/car/

regioneR: an R package for the management and comparison of genomic regions

Jit — Tue, 11 Dec 2018 08:43:51 -0600

Regioner is an R package for the management and comparison of genomic regions. It offers a set of function for basic manipulation of region sets extending the functionality of GenomicRanges and a powerful and customizable permutation test framework. With it, it's possible to study the association of a set of regions with other sets of regions, functions defined over the genome or essentially any user defined function.

http://gattaca.imppc.org/regioner/

Address of the bookmark: http://gattaca.imppc.org/regioner/

IgBLAST: a popular NCBI package for classifying and analyzing immunoglobulin (IG) and T cell receptor (TCR) variable domain sequences

BioJoker — Thu, 23 Jan 2020 11:34:37 -0600

NCBI team released a new version of IgBLAST with four new improvements. IgBLAST is a popular NCBI package for classifying and analyzing immunoglobulin (IG) and T cell receptor (TCR) variable domain sequences. Improvements are:

1. Support for the new FWR4 annotation feature in the AIRR format, both in standard format and in the AIRR alignment format.

2. The previous “-penalty” parameter was renamed as -V_penalty to be consistent with other IgBLAST penalty options.

3. Restored constant internal BLAST search parameters for domain annotation (i.e., FWR/CDR) such that this process is not influenced by user parameters.

4. Corrected FWR/CDR annotations for certain mouse VK and rat VH germline genes.

IgBLAST 1.15.0 is available for download from the BLAST FTP area. See the the new manual on GitHub for information about setting up and running IgBLAST.

If you have any questions or concerns, please contact blast-help@ncbi.nlm.nih.gov