BOL: Related items

jobTree based python wrapper to run the genome simulation tool suite Evolver

Jit — Fri, 08 Dec 2017 16:26:32 -0600

evolverSimControl (eSC) can be used to simulate multi-chromosome genome evolution on an arbitrary phylogeny (Newick format). In addition to simply running evolver, eSC also automatically creates statistical summaries of the simulation as it runs including text and image files. Also included are convenience scripts to: check on a running simulation and see detailed status and logging information; extract fasta sequence files from the leaf nodes of a completed simulation; extract pairwise multiple alignment files (.maf) from leaf and branch nodes from a completed simulation and with the help of mafJoin, join them together into a single maf covering the entire simulation.

Address of the bookmark: https://github.com/dentearl/evolverSimControl

Bioinformatician Dreams

Jitendra Narayan — Wed, 21 Aug 2013 10:50:45 -0500

Bioinformatician life is interconnected, they always dream for a powerful server, little more space on server as they are generating lots of data per run, dream to publish results in good impact journals, meetings reminders :) and research analysis off course!!!

AliTV—interactive visualization of whole genome comparisons

Jit — Wed, 10 Jan 2018 07:08:17 -0600

AliTV, which provides interactive visualization of whole genome alignments. AliTV reads multiple whole genome alignments or automatically generates alignments from the provided data. Optional feature annotations and phylo- genetic information are supported. The user-friendly, web-browser based and highly customizable interface allows rapid exploration and manipulation of the visualized data as well as the export of publication-ready high-quality figures. AliTV is freely available at https://github.com/AliTVTeam/AliTV

https://alitvteam.github.io/AliTV/

Address of the bookmark: https://github.com/AliTVTeam/AliTV

BIOINFORMATICS

Wed, 28 Aug 2013 19:16:33 -0500

This is a promo video for the brand new cross-boarder branch of study - BIOINFORMATICS. It´s a co-operation between Johannes Kepler University in Linz (Austria) and University of South Bohemia in České Budějovice (Czech Republic). Written, Edited and Directed by, DOP, VFX: Jan Míka Sound by: Mirek Šmilauer Narrator: Jack Bright Produced by: FILMOFON (http://www.filmofon.cz) Released: Nov 2012

G-compass: a comparative genome browser

Jit — Thu, 12 Apr 2018 10:00:27 -0500

G-compass (http://www.h-invitational.jp/g-compass/) is a comparative genome browser. It visualizes evolutionarily conserved genomic regions between human and other 12 vertebrates based on original genome alignments pursuing higher coverage (1,2). Annotations of human genes/transcripts and their ortholog information were derived from H-InvDB and its subdatabase Evola, respectively. G-compass is available for free of charge. [ Sample ]

Address of the bookmark: http://www.h-invitational.jp/g-compass/

R and Bioconductor Tutorial

Jitendra Narayan — Fri, 23 Aug 2013 08:23:59 -0500

This tutorial is intended to introduce users quickly to the basics of R, focusing on a few common tasks that biologists need to perform some basic analysis: load a table, plot some graphs, and perform some basic statistics. More extensive tutorials can be found on the project website and via bioconductor (not covered here).

You can add more tutorial links in comments if found new pages.

Address of the bookmark: http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual

P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads

Jit — Tue, 12 Jun 2018 08:14:41 -0500

P_RNA_scaffolder, a fast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This tool aims to improve the completeness of both protein-coding and non-coding genes. After this tool was applied to scaffolding human contigs, the structures of both protein-coding genes and circular RNAs were almost completely recovered and equivalent to those in a complete genome, especially for long proteins and long circular RNAs.

Address of the bookmark: http://www.fishbrowser.org/software/P_RNA_scaffolder/

What is Bioinformatics?

Wed, 28 Aug 2013 06:53:05 -0500

Illustration and Animation: Rachel Robinson Script: Tiffany Trent Voice-over: Kris Monger Sound: Glisten Carefully by Guennadi Malyshevski

IBM Research Computational Biology Center

Thu, 29 Aug 2013 08:43:59 -0500

The IBM Computational Biology Center embraces activities at Yorktown Heights, with strong affiliations with activities at Almaden and other IBM Research Centers. Computational Biology (CompBio) including bioinformatics is the study of how computer systems can manage, analyze, and simulate the complex structures and processes inherent in living systems. CompBio Research at IBM spans pattern recognition in sequences, structures and processes, the studying of systems ranging from single protein molecules through to complex molecular interactions, and the data analysis, interpretation and reverse-engineering of complex disease-lifestyle-genomic interactions for fuller biological understanding. "CompBio" has a flavor of its own independant of its parents, biology and computer science. Nonetheless, CompBio is inherently a multi- disciplinary field with important applications in biology, chemical physics, materials science, agriculture, chemistry and ultimately nanotechnology.

My commonly used commands in Bioinformatics

Rahul Nayak — Thu, 26 Jul 2018 04:58:45 -0500

FYI, I've found it useful to use MUMmer to extract the specific changes that Racon makes, so I can evaluate them individually:

minimap -t 24 assembly.fasta long_reads.fastq.gz | racon -t 24 long_reads.fastq.gz - assembly.fasta racon_assembly.fasta
nucmer -p nucmer assembly.fasta racon_assembly.fasta
show-snps -C -T -r nucmer.delta

This reports Racon's changes in a table. You can exclude indels with the -I option in show-snps.

This process (Racon -> MUMmer -> SNP table) solves the problem I originally raised in this issue. So as far as I'm concerned, you can close this issue (or keep it open if you still want to implement some kind of variant table).