BOL: Related items

Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life

Abhimanyu Singh — Fri, 02 Nov 2018 08:16:27 -0500

Ancestral Genomes (http://ancestralgenomes.org) is a resource for comprehensive reconstructions of these ‘fossil genomes’. Comprehensive sets of protein-coding genes have been reconstructed for 78 genomes of now-extinct species that were the common ancestors of extant species from across the tree of life.

Address of the bookmark: http://ancestralgenomes.org/

Translational Bioinformatics: Transforming 300 Billion Points of Data

Tue, 20 Aug 2013 19:03:47 -0500

Translational Bioinformatics: Transforming 300 Billion Points of Data into Diagnostics, Therapeutics, and New Insights into Disease Air date: Wednesday, June 20, 2012, 3:00:00 PM Time displayed is Eastern Time, Washington DC Local Description: There is an urgent need to translate genome-era discoveries into clinical utility, but the difficulties in making bench-to-bedside translations haven't been well described. The nascent field of translational bioinformatics may help. Dr. Butte's lab at Stanford University builds and applies tools that convert more than 300 billion points of molecular, clinical, and epidemiological data (measured by researchers and clinicians over the past decade) into diagnostics, therapeutics, and new insights into disease. Dr. Butte, a bioinformatician and pediatric endocrinologist, will highlight his lab's work on using publicly available molecular measurements to find new uses for drugs, discovering new treatable mechanisms of disease in type 2 diabetes, and evaluating patients presenting with whole genomes sequenced. The NIH Wednesday Afternoon Lecture Series includes weekly scientific talks by some of the top researchers in the biomedical sciences worldwide. For more information, visit: The NIH Director's Wednesday Afternoon Lecture Series Author: Atul Butte, M.D., Ph.D., Stanford University Runtime: 01:07:42 Permanent link: http://videocast.nih.gov/launch.asp?17321

ANGES: reconstructing ANcestral GEnomeS maps

Abhimanyu Singh — Thu, 18 May 2017 05:27:08 -0500

This page contains the software ANGES 1.01, that aims at reconstucting ancestral genome maps from homologous markers in extant related genomes.

Download

Program, version 1.01 (July 10, 2012, documentation updated in August 2014)
Examples with results (featured ancestors: boreoeutherian, amniote, yeasts, Burkholderia, monocots); please refer to the documentation of the distribution above.

Address of the bookmark: http://paleogenomics.irmacs.sfu.ca/ANGES/

dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.

Jit — Wed, 20 Dec 2017 18:35:16 -0600

While the number of sequenced diploid genomes have been steadily increasing in the last few years, assembly of highly polymorphic (HP) diploid genomes remains challenging. As a result, there is a shortage of tools for assembling HP genomes from the next generation sequencing (NGS) data. The initial approaches to assembling HP genomes were proposed in the pre-NGS era and are not well suited for NGS projects. To address this limitation, we developed the first de Bruijn graph assembler, dipSPAdes, for HP genomes that significantly improves on the state-of-the-art assemblers for HP diploid genomes.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pubmed/25734602

D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way

Jit — Mon, 11 Jun 2018 09:41:22 -0500

D-GENIES – for Dotplot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualisation. We use minimap version 2 to align the two genomes. Then, the PAF file is parsed and plotted into an interactive plot written with d3.js library. D-Genies also allows to display dot plots from other aligners by uploading their PAF or MAF alignment file. http://dgenies.toulouse.inra.fr/

Address of the bookmark: http://dgenies.toulouse.inra.fr/

P10K: The Protist 10,000 Genomes

BioStar — Sat, 06 Jul 2024 08:29:30 -0500

The Protist 10,000 Genomes (P10K) Project aims to decipher the genome sequences and construct a comprehensive database resource containing over 10,000 species of protists, encompassing representatives from every major clade. Samples were collected from diverse habitats, and the genome information was acquired through de novo sequencing, genome re-annotation, and integration of publicly available data. Serving as a centralized data portal for the project, the P10K database primarily focuses on delivering high-quality curation and facilitating efficient retrieval of protist genome data.

Address of the bookmark: https://ngdc.cncb.ac.cn/p10k/

GView: A Java application for viewing and examining prokaryotic genomes in a circular or linear context

Abhimanyu Singh — Fri, 14 Jul 2017 07:47:03 -0500

GView is a Java application for viewing and examining prokaryotic genomes in a circular or linear context. It accepts standard sequence file formats and an optional style specification file to generate customizable, publication quality genome maps in bitmap and scalable vector graphics formats. GView features an interactive pan-and-zoom interface, a command-line interface for incorporation in genome analysis pipelines, and a public Application Programming Interface for incorporation in other Java applications.

Availability: GView is a freely available application licensed under the GNU Public License. The application, source code, documentation, file specifications, tutorials and image galleries are available at http://gview.ca

Contact: ac.cg.cpsa-cahp@raalesmod.nav.yrag

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995121/

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995121/

kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome

Jit — Fri, 08 Dec 2017 16:48:40 -0600

Sept. 20, 2017 Version 3.1 released. Major upgrade. Version 3.1 fixes the problems with SNP annotation that arose when NCBI discontinued use of GI numbers. Please read carefully the Preface (page 3) and the File of annotated genomes section (pages 9-10) in the version 3.1 User Guide. Thanks to Tom Slezak for revsing the get_genbank_file3 script and to Tod Stuber (USDA) for testing version 3.1 even though he doesn't need the annotation feature. All users are encouraged to upgrade to version 3.1.

Address of the bookmark: https://sourceforge.net/projects/ksnp/files/

Tallymer: method to compute K-mer frequencies and its application to annotate large repetitive plant genomes

Jit — Thu, 15 Feb 2018 10:21:02 -0600

Tallymer is based on enhanced suffix arrays. This gives a much larger flexibility concerning the choice of the k-mer size. Tallymer can process large data sizes of several billion bases. We used it in a variety of applications to study the genomes of maize and other plant species. In particular, Tallymer was used to index a set whole genome shotgun sequences from maize (B73) (total size 10⁹ bp).
Tallymer was effective in a variety of applications to aid genome annotation in maize, despite limitations imposed by the relatively low coverage of sequence available.

A manual can be found here.

Address of the bookmark: https://www.zbh.uni-hamburg.de/forschung/arbeitsgruppe-genominformatik/software/tallymer.html

GenomeMapper: Simultaneous alignment of short reads against multiple genomes

Jit — Fri, 25 May 2018 09:29:44 -0500

GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single reference. If you are unsure which one is the appropriate GenomeMapper, you might want to use the latter https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768987/

Address of the bookmark: http://1001genomes.org/software/genomemapper.html