BOL: All site bookmarks

REGEN: Ancestral Genome Reconstruction for Bacteria

Rahul Nayak — Tue, 06 Mar 2018 05:02:36 -0600

REGEN infers evolutionary events, including gene creation and deletion and replicon fission and fusion. The reconstruction can be performed by either a maximum parsimony or a maximum likelihood method. Gene content reconstruction is based on the concept of neighboring gene pairs. REGEN was designed to be used with any set of genomes that are sufficiently related, which will usually be the case for bacteria within the same taxonomic order.

Address of the bookmark: http://www.mdpi.com/2073-4425/3/3/423

scikit-bio™ is an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics.

Jit — Fri, 02 Mar 2018 04:29:47 -0600

scikit-bio is currently in beta. We are very actively developing it, and backward-incompatible interface changes can and will arise. To avoid these types of changes being a surprise to our users, our public APIs are decorated to make it clear to users when an API can be relied upon (stable) and when it may be subject to change (experimental). See the API stability docs for more details, including what we mean by stable and experimental in this context.

Address of the bookmark: http://scikit-bio.org/

An Introduction to Applied Bioinformatics

Jit — Fri, 02 Mar 2018 04:26:38 -0600

IAB is primarily being developed by Greg Caporaso(GitHub/Twitter: @gregcaporaso) in the Caporaso Lab at Northern Arizona University. You can find information on the courses I teach on my teaching website and information on my research and lab on my lab website.

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

Protein Subcellular Localization Prediction

Poonam Mahapatra — Thu, 01 Mar 2018 06:20:47 -0600

Assigning subcellular localization to a protein is an important step towards elucidating its interaction partners, function, and potential role(s) in the cellular machinery. Computational tools offer an attractive complement to time-consuming and laborious experimental methods.

http://abi.inf.uni-tuebingen.de/Services/YLoc/webloc.cgi

Address of the bookmark: https://abi.inf.uni-tuebingen.de/Research/Systems%20Biology/protein-subcellular-localization

Generate interactive codon usage plots

Jit — Wed, 28 Feb 2018 03:47:40 -0600

Generate interactive codon usage plots as used at ensembl.lepbase.org. The input file format can be generated from an Ensembl database using the export_json.pl script from the easy-import pipeline.

live demo

Address of the bookmark: https://github.com/rjchallis/codon-usage

Genome assembly stats plotting

Jit — Wed, 28 Feb 2018 03:45:39 -0600

A de novo genome assembly can be summarised b

y a number of metrics, including:

Overall assembly length
Number of scaffolds/contigs
Length of longest scaffold/contig
Scaffold/contig N50 and N90Assembly base composition, in particular percentage GC and percentage Ns
CEGMA completeness
Scaffold/contig length/count distribution

assembly-stats supports two widely used presentations of these values, tabular and cumulative length plots, and introduces an additional circular plot that summarises most commonly used assembly metrics in a single visualisation. Each of these presentations is generated using javascript from a common (JSON) data structure, allowing toggling between alternative views, and each can be applied to a single or multiple assemblies to allow direct comparison of alternate assemblies.

Tabular presentation allows direct comparison of exact values between assemblies, the limitations of this approach lie in the necessary omission of distributions and the challenge of interpreting ratios of values that may vary by several orders of magnitude.

Address of the bookmark: https://github.com/rjchallis/assembly-stats

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

Jit — Mon, 19 Feb 2018 06:46:15 -0600

ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics.

The new features include

(i) building gene-based and supermatrix-based phylogenies using a single command,

(ii) testing and visualizing evolutionary models,

(iii) calculating distances between trees of different size or including duplications, and

(iv) providing seamless integration with the NCBI taxonomy database.

ETE is freely available at http://etetoolkit.org

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

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

MeDuSa: a multi-draft based scaffolder

Abhimanyu Singh — Wed, 14 Feb 2018 02:49:00 -0600

MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained from a set of (draft or closed) genomes from related organisms to determine the correct order and orientation of the contigs. MeDuSa formalises the scaffolding problem by means of a combinatorial optimisation formulation on graphs and implements an efficient constant factor approximation algorithm to solve it. In contrast to currently used scaffolders, it does not require either prior knowledge on the microrganisms dataset under analysis (e.g. their phylogenetic relationships) or the availability of paired end read libraries.

Address of the bookmark: https://github.com/combogenomics/medusa

circosJS: d3 library to build circular graphs

Jit — Tue, 13 Feb 2018 06:57:32 -0600

Circos is a javascript library to easily build interactive graphs in a circular layout. It's based on d3.js. It aims to be a javascript version of the Circos software.

You should consider using Circos to show:

relationships between entities
periodical data

Address of the bookmark: https://github.com/nicgirault/circosJS