BOL: Related items

HivePlot

Jit — Thu, 16 Feb 2017 11:39:34 -0600

The hive plot is a rational visualization method for drawing networks. Nodes are mapped to and positioned on radially distributed linear axes — this mapping is based on network structural properties. Edges are drawn as curved links. Simple and interpretable.

The purpose of the hive plot is to establish a new baseline for visualization of large networks — a method that is both general and tunable and useful as a starting point in visually exploring network structure.

More at http://www.hiveplot.com/

Address of the bookmark: http://www.hiveplot.com/

GenomeComp

Jit — Fri, 17 Feb 2017 08:38:32 -0600

GenomeComp is a tool for summarizing, parsing and visualizing the genome wide sequence comparison results derived from voluminous BLAST textual output, so as to locate the rearrangements, insertions or deletions of genome segments between species or strains.

It can be easily used to compare, parsing and visualize large genomic sequences, especially closely related genomes such as inter-species or inter-strains. In addition, it can also show other sequence features like repeat sequence distributions in one whole-genome DNA sequence by comparing the genome to itself.

It is a stand-alone graphical user interface (GUI) program which runs on Linux, Unix, Mac OS X (tested on version 10.2.4 only) and Microsoft Windows platforms and is written in Perl/Tk.

Address of the bookmark: http://www.mgc.ac.cn/GenomeComp/

DIAL

Abhimanyu Singh — Wed, 01 Mar 2017 08:42:28 -0600

A computational pipeline for identifying single-base substitutions between two closely related genomes without the help of a reference genome. DIAL works even when the depth of coverage is insufficient for de novo assembly, and it can be extended to determine small insertions/deletions. Our main motivation is to use this tool to survey the genetic diversity of endangered species as the identified sequence differences can be used to design genotyping arrays to assist in the species' management.

http://www.bx.psu.edu/~ratan/

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

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/

Ancestral sequence reconstruction steps !

Surabhi Chaudhary — Fri, 18 May 2018 08:28:26 -0500

Ancestral sequence reconstruction (ASR) – also known as ancestral gene/sequence reconstruction/resurrection – is a technique used in the study of molecular evolution. The method consists of the synthesis of an ancestral gene and expression of the corresponding ancestral protein. The idea of protein 'resurrection' was suggested in 1963 by Pauling and Zuckerkandl. Some early efforts were made in the eighties-nineties, led by the laboratory of Steven A. Benner, showing the potential of this technique – one that only started to be fulfilled in the post-genomic era. Thanks to the improvement of algorithms and of better sequencing and synthesis techniques, the method was developed further in the early 2000s to allow the resurrection of a greater variety of and much more ancient genes. Over the last decade, ancestral protein resurrection has developed as a strategy to reveal the mechanisms and dynamics of protein evolution.

BEAST is the best way to predict the ancestral structure. but, I suggest following steps?

1- Alignments "Mafft - http://mafft.cbrc.jp/alignment/software/source.html"

mafft --maxiterate 1000 --reorder --thread 24 --genafpair Dataset.fasta > Dataset_Alig.fasta

2- Your dataset has a good phylogenetic signal, is possible to perform with Tree-Puzzle "http://www.tree-puzzle.de";

3 - This dataset which the saturation index, I perform with "http://dambe.bio.uottawa.ca/dambe.asp";

4- Has evidence of possible recombination in your dataset, the evaluate if this presence or absence, because this may to influence the grouping of clades, I perform with

---recombination

4.1- Phi-test, implemented in SplitTree4"http://www.splitstree.org", (.nex file)

4.2- GARD deployed in webserver in the DataMonkey "http://www.datamonkey.org/" - turning to the amino acid seaview -> view proteins -> save as ...) Ideally do a tree-based groups.

4.3- RDP4 for download and installation on Windows in "http://web.cbio.uct.ac.za/~darren/rdp.html"

4.4- Hyphy (Mac, Windows, Linux) in "http://hyphy.org/w/index.php/Download"

4.5- Path-o-Gen (temporal structure of a tree input file -> arquivo.tre)

These steps above, I call of pre-processing to inferences phylogenetic...

5- Perform phylogenetic tree, used Bayesian Inference with Molecular Clock, but is necessary Clock Testing:

- This step is performed with program Beast (Beauti, Beast and TreeAnnotator), and Tracer_v1.5 more FigTree to inspection.

- Tutorials: http://beast.bio.ed.ac.uk/tutorials

- Downloads: http://beast.bio.ed.ac.uk/downloads

Multi-metagenome assembly

Radha Agarkar — Fri, 03 Mar 2017 10:14:18 -0600

This project contains scripts and tutorials on how to assemble individual microbial genomes from metagenomes, as described in:

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

Mads Albertsen, Philip Hugenholtz, Adam Skarshewski, Gene W. Tyson, Kåre L. Nielsen and Per .H. Nielsen

Nature Biotechnology 2013, doi: 10.1038/nbt.2579

Address of the bookmark: https://github.com/MadsAlbertsen/multi-metagenome

CONCOCT: Clustering cONtigs with COverage and ComposiTion

Jit — Mon, 06 Mar 2017 04:08:16 -0600

A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.

Warning! This software is to be considered under development. Functionality and the user interface may still change significantly from one version to another. If you want to use this software, please stay up to date with the list of known issues:https://github.com/BinPro/CONCOCT/issues

Address of the bookmark: https://github.com/BinPro/CONCOCT

SeqMule: Automated human exome/genome variants detection

Abhimanyu Singh — Tue, 07 Mar 2017 10:12:36 -0600

SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its configuration file. SeqMule also has some built-in functions, such as pooling consensus calls from various callers, plotting a Venn diagram showing intersection among different callers, and downloading databases. SeqMule can be used for both Mendelian disease study and cancer genome study.

Address of the bookmark: http://seqmule.openbioinformatics.org/en/latest/

gbtools: Interactive Visualization of Metagenome Bins in R

Jit — Sun, 26 Mar 2017 15:41:31 -0500

We have developed gbtools, a software package that allows users to visualize metagenomic assemblies by plotting coverage (sequencing depth) and GC values of contigs, and also to annotate the plots with taxonomic information. Different sets of annotations, including taxonomic assignments from conserved marker genes or SSU rRNA genes, can be imported simultaneously; users can choose which annotations to plot. Bins can be manually defined from plots, or be imported from third-party binning tools and overlaid onto plots, such that results from different methods can be compared side-by-side. gbtools reports summary statistics of bins including marker gene completeness, and allows the user to add or subtract bins with each other.

Tool at https://github.com/kbseah/genome-bin-tools

Address of the bookmark: http://journal.frontiersin.org/article/10.3389/fmicb.2015.01451/full

DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies

Jit — Wed, 19 Apr 2017 10:09:51 -0500

DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies

Our work is published in Scientific Reports:

Ye, C. et al. DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies. Sci. Rep. 6, 31900; doi: 10.1038/srep31900 (2016).

http://www.nature.com/articles/srep31900

The manual can be downloaded from:

https://github.com/yechengxi/DBG2OLC/raw/master/Manual.docx

To use precompiled versions,please go to:

https://github.com/yechengxi/DBG2OLC/tree/master/compiled

Address of the bookmark: https://github.com/yechengxi/DBG2OLC