BOL: Related items

SIMBA: a Genome Assembly Project Management System

Neel — Thu, 29 Nov 2018 08:52:25 -0600

SIMBA, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS) platforms quickly, easily and effectively. SIMBA also is open source tool, i.e., can be freely downloaded, shared and modified.

Address of the bookmark: http://ufmg-simba.sourceforge.net/

Senior Bioinformatician (Assembly) Moore Aquatic Symbiosis Project Tree of Life

Sat, 02 Oct 2021 00:28:30 -0500

You will have some previous experience with genome bioinformatics or other large scale scientific data analysis, or a newly qualified graduate student with data science skills interested in DNA sequence data. While desirable, previous experience with DNA sequencing data is not strictly necessary for the position. We have a strong publication record and culture of producing open data resources and open source software development. This role requires an investigative and solution-oriented mindset and excellent communication skills to work effectively within large national and international consortia.

More at https://jobs.sanger.ac.uk/vacancy/senior-bioinformatician-assembly-moore-aquatic-symbiosis-project-tree-of-life-458923.html

The Breeding API (BrAPI) project

BioStar — Wed, 06 Jan 2021 19:51:17 -0600

The Breeding API (BrAPI) project is an effort to enable interoperability among plant breeding databases. BrAPI is a standardized RESTful web service API specification for communicating plant breeding data. This community driven standard is free to be used by anyone interested in plant breeding data management.

Address of the bookmark: https://brapi.org/

Postdoctoral Position in Evolutionary Genomics and Bioinformatics, at the Center for Interdisciplinary Neuroscience at University of Valparaiso, Valparaiso, Chile.

Wed, 22 Apr 2026 02:36:00 -0500

The Center for Interdisciplinary Neuroscience of Valparaiso (CINV)
in Valparaiso, Chile, invites postdoctoral researchers to apply for
a Postdoctoral Fellowship focusing on understanding the evolution of
genes and molecular pathways that play a role on inflammatory processes
driving diseases affecting the central nervous system.

The postdoctoral researcher will contribute to this project using
a combination of evolutionary and comparative genomics, as well as a
diverse set of bioinformatic approaches for data analysis and integration
(e.g., transcriptomics, genomics, phenotypic data). This position offers
a unique opportunity to integrate diverse state-of-the-art genomic and
phenotypic datasets across different model organisms to understand the
role of genes, molecular pathways in the origin of complex diseases.

CINV provides a highly collaborative and multidisciplinary environment
using a variety of computational and experimental approaches,
including genetically tractable animal models as well as expertise in
genetics, behavior, glia-neuron communication, metabolism, biophysics,
genomics, bioinformatics, host-microbe communication, and biomolecular
modelling. The new postdoc will be part of one of our labs which focuses
more generally on the intersection between molecular evolution and
disease biology.

Required qualifications are a PhD in evolutionary biology, computational
biology, bioinformatics, or closely related fields. Candidates must have
excellent verbal and written communication skills (working language
is English), as well as an established record of productivity (e.g.,
at least one previous peer-reviewed publication). Candidates with a
past record of publications in bioinfomatics, computational biology,
population genetics or evolutionary genomics are strongly preferred. Ideal
candidates should have experience in analyzing genomic and phenomic
data, performing comparative evolution or population genomic analyses,
as well as in collaborating with experimentalists.

Interested candidates should first contact Evandro Ferrada at
. Please include the following: (1) a cover
letter addressing your interest in the position and how your expertise
meets the position requirements, (2) a CV, (3) contact information of
at least 2 references. A short online interview will follow to discuss
specific proposals. Candidate materials will be reviewed as soon as
possible until the position is filled.

For further information, please visit:
https://cinv.uv.cl/cinv-postdoctoral-fellowship-program-2026/

Dr. Evandro Ferrada
Associate Profesor

Centro Interdisciplinario de Neurociencia (CINV)

Facultad de Ciencias, Universidad de Valpara�so.

Pasaje Harrington 287, Playa Ancha, Valpara�so, Chile.

Tel. +56 (32) 250 8453

www.cinv.cl

DAGchainer: Computing Chains of Syntenic Genes in Complete Genomes

Abhimanyu Singh — Fri, 17 Feb 2017 16:13:35 -0600

The DAGchainer software computes chains of syntenic genes found within complete genome sequences. As input, DAGchainer accepts a list of gene pairs with sequence homology along with their genome coordinates. Using a scoring function which accounts for the distance between neighboring genes on each DNA molecule and the BLAST E-value score between homologs, maximally scoring chains of ordered gene pairs are computed and reported. This algorithm can be used to mine large evolutionary conserved regions of genomes between two organisms. Alternatively, by examining colinear sets of homologous genes found within a single genome, segmental genome duplications can be revealed.

This software distribution includes both the DAGchainer utility and a Java-based graphical interface that allows the inputs and outputs to be navigated and interrogated dynamically.

Address of the bookmark: http://dagchainer.sourceforge.net/

GOLD:Genomes Online Database

Jit — Wed, 26 Jul 2017 07:49:29 -0500

GOLD:Genomes Online Database, is a World Wide Web resource for comprehensive access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world.

https://gold.jgi.doe.gov/

Address of the bookmark: https://gold.jgi.doe.gov/

Understanding liftOver !

Rahul Nayak — Wed, 06 Jun 2018 10:00:20 -0500

LiftOver is a necesary step to bring all genetical analysis to the same reference build. LiftOver can have three use cases:

(1) Convert genome position from one genome assembly to another genome assembly

In most scenarios, we have known genome positions in NCBI build 36 (UCSC hg 18) and hope to lift them over to NCBI build 37 (UCSC hg19).

(2) Convert dbSNP rs number from one build to another

(3) Convert both genome position and dbSNP rs number over different versions

Run:

liftOver input.bed hg18ToHg19.over.chain.gz output.bed unlifted.bed

The outformat is as follow:

Deleted in new:
    Sequence intersects no chains
Partially deleted in new:
    Sequence insufficiently intersects one chain
Split in new:
    Sequence insufficiently intersects multiple chains
Duplicated in new:
    Sequence sufficiently intersects multiple chains
Boundary problem:
    Missing start or end base in an exon

For example:

If you liftOver chr4:6497-6497 from hg19 to GRch38 and it return "deleted in new".

It means chr4:6497-6497 is part of a genomic contig on hg19 that is not anymore mapped on GRch38 because the new assembly is now better built without including this contig.

DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies

Shruti Paniwala — Fri, 03 Jan 2020 13:28:19 -0600

DeCoSTAR computes adjacency evolutionary scenarios using a scoring scheme based on a weighted sum of adjacency gains and breakages. Solutions, both optimal and near-optimal, are sampled according to the Boltzmann–Gibbs distribution centered around parsimonious solutions, and statistical supports on ancestral and extant adjacencies are provided. DeCoSTAR supports the features of previously contributed tools that reconstruct ancestral adjacencies, namely DeCo, DeCoLT, ART-DeCo, and DeClone. In a few minutes, DeCoSTAR can reconstruct the evolutionary history of domains inside genes, of gene fusion and fission events, or of gene order along chromosomes, for large data sets including dozens of whole genomes from all kingdoms of life.

Address of the bookmark: https://github.com/YoannAnselmetti/DeCoSTAR_pipeline

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/

Harvest: a suite of core-genome alignment and visualization tools

Jit — Fri, 08 Dec 2017 07:16:03 -0600

Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees.

Tools

Parsnp - Core-genome alignment and analysis
Gingr - Interactive visualization of alignments, trees and variants
HarvestTools - Archiving and postprocessing

Address of the bookmark: https://harvest.readthedocs.io/en/latest/