BOL: Related items

Nemo – A stochastic, individual-base, genetically explicit simulation platform

Jit — Sat, 01 Oct 2016 14:45:02 -0500

A recombination map has been added for all multi-locus traits. The map positions (chromosomal) for neutral markers (e.g. SNPs) and loci under selection (QTLs, deleterious mutations, DMIs) can now be specified explicitly, or set at random. The map can hold an unlimited number of loci of different types jointly, at any recombination scale (cM or lower). The effects of linkage can thus be finely explored.
A new trait coding for (Bateson-)Dobzhansky-Muller incompatibility loci. Multiple haploid or diploid pairs of incompatible loci can be spread throughout the genome and affect individual fitness.
Multi-type selection: Individual fitness can be jointly determined by different types of loci under selectinon, such as QTLs coding for quantitative traits under spatially variable selection, universally deleterious mutations, and Dobzhansky-Muller incompatibility loci.
An unlimited number of quantitative traits under different forms of selection can be modelled, based on universally pleiotropic loci with several bi- or multi-allelic models.
Spatial and temporal variation of selection on quantitative traits is possible, modelling shifts of environmental conditions over time.
The dispersal matrix describing the movement of individuals among sub-populations can be replaced by a connectivity matrix and a reduced dispersal matrix describing migration only among the connected sub-populations. This offers a substantial gain in computing time and system memory when simulating very large grids.
Input parameters' arguments may be specified in separate files. This is particularly convenient when specifying large matrices.
Many adjustments have been made for refined control of the input of parameters and data output. See updates in the manual.

Address of the bookmark: http://nemo2.sourceforge.net/index.html

PHYMMBL

Jit — Mon, 10 Oct 2016 08:56:34 -0500

Metagenomics sequencing projects collect samples of DNA from uncharacterized environments that may contain hundreds or even thousands of species. One of the main challenges in analyzing a metagenome is phylogenetic classification of raw sequence reads into groups representing the same or similar species. Such classification is a useful prerequisite for genome assembly and for analysis of the biological diversity present in a sample. The newest sequencing technologies have simultaneously made metagenomics easier, by making the sequencing process faster, and more difficult, by producing shorter read lengths than previous technologies. Methods for classifying sequences as short as 100 base pairs (bp) have until now been relatively inaccurate, requiring metagenomics projects to use older, long-read technologies. Phymm, a new classification approach for metagenomics data which uses interpolated Markov models (IMMs) to taxonomically classify DNA sequences, can accurately classify reads as short as 100 bp. Its accuracy for short reads represents a significant leap forward over previous composition-based classification methods. PhymmBL (rhymes with "thimble"), the hybrid classifier included in this distribution which combines analysis from both Phymm and BLAST, produces even higher accuracy.

Address of the bookmark: http://www.cbcb.umd.edu/software/phymm/

eFORGE.v1.2

Jit — Fri, 28 Oct 2016 09:06:59 -0500

The eFORGE tool provides a method to view the tissue specific regulatory component of a set of EWAS DMPs. eFORGE analysis takes a set of DMPs, such as those hits above genome-wide significance threshold in an EWAS study, and analyses whether there is enrichment for overlap of putative functional elements compared to matched background DMPs. It assesses enrichment on a per cell type basis, since functional elements are differentially active in different cell types, and hence can expose tissue-specific signals of enrichment for the given test DMP set. This can reveal the sites of action underlying the EWAS signal, and provide confirmation of the validity of the EWAS where a tissue-specific mechanism is known or expected for the phenotype. Conversely unknown tissue involvements can also be revealed.

Address of the bookmark: http://eforge.cs.ucl.ac.uk/eFORGE.v1.2/?documentation

e-RGA: enhanced Reference Guided Assembly of Complex Genomes

Jit — Mon, 19 Dec 2016 05:56:14 -0600

Next Generation Sequencing has totally changed genomics: we are able to produce huge amounts of data at an incredibly low cost compared to Sanger sequencing. Despite this, some old problems have become even more difficult, de novo assembly being on top of this list. Despite efforts to design tools able to assemble, de novo, an organism sequenced with short reads, the results are still far from those achievable with long reads. In this paper, we propose a novel method that aims to improve de novo assembly in the presence of a closely related reference. The idea is to combine de novo and reference-guided assembly in order to obtain enhanced results.

Address of the bookmark: http://journal.embnet.org/index.php/embnetjournal/article/view/208

sockeye

Jit — Fri, 17 Feb 2017 08:51:16 -0600

This sockeye software uses the Ensembl database project to import sequence and annotation information from several eukaryotic species. A user can additionally import their own custom sequence and annotation data. Individual annotation objects are displayed in Sockeye by using custom 3D models. Ensembl-derived and imported sequences can be analyzed by using a suite of multiple and pair-wise alignment algorithms. The results of these comparative analyses are also displayed in the 3D environment of Sockeye. By using the Java3D API to visualize genomic data in a 3D environment, we are able to compactly display cross-sequence comparisons. This provides the user with a novel platform for visualizing and comparing genomic feature organization.

Address of the bookmark: http://www.bcgsc.ca/platform/bioinfo/software/sockeye/releases/1.3

VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity

Abhimanyu Singh — Tue, 30 Oct 2018 10:46:28 -0500

VGSC, the Vector Graph toolkit of genome Synteny and Collinearity, and its online service, to visualize the synteny and collinearity in the common graphical format, including both raster (JPEG, Bitmap, and PNG) and vector graphic (SVG, EPS, and PDF).

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4783527/

Entire Human Genome Sequencing !

LEGE — Tue, 02 Apr 2024 01:19:29 -0500

Cost-effective whole human genome sequencing has revolutionized the landscape of genetic research and personalized medicine by making comprehensive genetic analysis accessible to a wider population. Through advancements in sequencing technologies, such as next-generation sequencing (NGS), costs have significantly decreased, enabling researchers and healthcare providers to analyze an individual's complete genetic makeup with greater efficiency and affordability. This has profound implications for disease diagnosis, prognosis, and treatment, as it allows for the identification of genetic predispositions and the customization of healthcare interventions based on an individual's unique genetic profile. Moreover, as the cost continues to decline, the potential for population-scale genomic studies and large-scale screening programs becomes increasingly feasible, promising to further enhance our understanding of human genetics and improve healthcare outcomes on a global scale.

Here are few companies:

https://mynucleus.com/

https://myome.com/

https://nebula.org/whole-genome-sequencing-dna-test/

Scaffolding of a bacterial genome using MinION nanopore sequencing

Rahul Agarwal — Tue, 07 Jul 2015 16:59:25 -0500

Second generation sequencing has revolutionized genomic studies. However, most genomes contain repeated DNA elements that are longer than the read lengths achievable with typical sequencers, so the genomic order of several generated contigs cannot be easily resolved. A new generation of sequencers offering substantially longer reads is emerging, notably the Pacific Biosciences (PacBio) RS II system and the MinION system, released in early 2014 by Oxford Nanopore Technologies through an early access program.

Address of the bookmark: http://www.nature.com/srep/2015/150707/srep11996/full/srep11996.html

QuIN’s web server

Jit — Mon, 27 Jun 2016 10:44:16 -0500

Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers) at distal genomic locations can interact with each other via chromatin folding and affect gene expression levels. Genomic technologies for mapping interactions between DNA regions, e.g., ChIA-PET and HiC, can generate genome-wide maps of interactions between regulatory elements. These interaction datasets are important resources to infer distal gene targets of non-coding regulatory elements and to facilitate prioritization of critical loci for important cellular functions. With the increasing diversity and complexity of genomic information and public ontologies, making sense of these datasets demands integrative and easy-to-use software tools. Moreover, network representation of chromatin interaction maps enables effective data visualization, integration, and mining. Currently, there is no software that can take full advantage of network theory approaches for the analysis of chromatin interaction datasets. To fill this gap, we developed a web-based application, QuIN, which enables: 1) building and visualizing chromatin interaction networks, 2) annotating networks with user-provided private and publicly available functional genomics and interaction datasets, 3) querying network components based on gene name or chromosome location, and 4) utilizing network based measures to identify and prioritize critical regulatory targets and their direct and indirect interactions.

AVAILABILITY: QuIN’s web server is available at http://quin.jax.org QuIN is developed in Java and JavaScript, utilizing an Apache Tomcat web server and MySQL database and the source code is available under the GPLV3 license available on GitHub:https://github.com/UcarLab/QuIN/.

Address of the bookmark: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004809

Fancy Oneliner for Bioinformatics !!

Poonam Mahapatra — Thu, 07 Jul 2016 12:05:50 -0500

This webpage lists some of the one-liners that we frequently use in metagenomic analyses. You can click on the following links to browse through different topics. You can copy/paste the commands as they are in your terminal screen, provided you follow the same naming conventions and folder structures as we have. We are sharing these codes with the intention that if they are useful and help you in your analyses, then we will be appropriately credited as considerable effort has been put into devising them.

Address of the bookmark: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/oneliners.html