BOL: Related items

GFinisher: a new strategy to refine and finish bacterial genome assemblies

Jit — Thu, 26 Jul 2018 09:31:55 -0500

GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes the contigs/scaffolds with genomes references.

java -Xms2G -Xmx4G -jar GenomeFinisher.jar  \
    -i target_contigs.fasta  \
    -ds alternative_assemblies.fasta -ref reference.fasta  \
    -o outputDirectory

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

MITOS: improved de novo metazoan mitochondrial genome annotation

Jit — Fri, 26 Oct 2018 08:25:39 -0500

Allows automatic annotation of metazoan mitochondrial genomes. MITOS is a pipeline designed to compute a consistent de novo annotation of the mitogenomic sequences. The software allows for a systematic error screening, the standardisation of gene name and gene boundary designation, anticodon labelling of tRNAs, and provides the means for the assessment of the validity of a gene assignment.

Address of the bookmark: http://mitos.bioinf.uni-leipzig.de/index.py

Postdoc Position in Computational Biology

Fri, 14 Mar 2014 01:38:49 -0500

The Computational Biology Group of Interdisciplinary Center for
Clinical Research (IZKF) Aachen, RWTH Aachen University Hospital,
Aachen, invites applicants for PhD candidate or postdoctoral position
in computational biology in one of the following topics:

1) Statistical machine learning methods for the analysis of medical
epigenomics data.

2) Sequence analysis algorithms for detection of RNA-DNA interactions.

Applicants should hold a M.Sc . or PhD in Computer Science or related
areas. Experience in the analysis of biological sequences, gene
expression and gene regulation is desirable. The candidate should have
solid programming skills (C, Python and/or R) and acquaintance with
Linux. Experience with high performance computing is a plus. The
working language of the group is English.

The position is based on the German TV-L 13 salary scale, including
all German social benefits (health insurance and pension scheme). The
expected starting date is September 2014. Interested candidates should
send a CV, statement of research interests and the names of three
references to jobs@costalab.org.

More at http://costalab.org/wp/phd-and-postdoc-position-in-computational-biology/

ASCIIGenome: genome browser based on command line interface and designed for running from console terminals.

Neel — Fri, 09 Nov 2018 13:50:04 -0600

ASCIIGenome is a genome browser based on command line interface and designed for running from console terminals.

Since ASCIIGenome does not require a graphical interface it is particularly useful for quickly visualizing genomic data on remote servers while offering flexibility similar to popular GUI viewers like IGV.

Documentation is at readthedocs/asciigenome.

Address of the bookmark: https://github.com/dariober/ASCIIGenome

BioGeek Fun

Jit — Sun, 16 Mar 2014 06:33:31 -0500

1. A futuristic computational biology student was told to write "It is in my gene!!!" on the board 100 times as a punishment. here's his response -

use warnings;
for ($count=1; $count <=100; $count++) { print "It is in my gene!!!";}

I guess, he is gonna to be a real biogeek. Nice try though. Smart kid.

2. In some perl script I found this
. . . . . .
. . . . . .
# It works for me, only God understood how it is working
while (/(<\/[^>]+>)|(<[^>]+>)|(<[^>]+>)$|([^><]+)/go) {
            $startGene=$1;
            $beginChromosome=$2;

. . . . . .
.. . . . . .
}

3. One more interesting message in Perl found …. It will must tickle you bone :)
open(my $fh, "<", "gene.txt") or kill " Me if you think this is a mistake :$!";

4. From the Perl

while () { # "The Mothership Connection is here!"
print “$_\n”; # Printing the offspring :)

5. Perl message
if ($1) { print “Just found a the error in chromosome !!!, yahoo…”; else { “That is not error, but mutation you moron!”;

6. One genome database curator walk in wine bar asked the bartender:
CREATE TABLE gene IF NOT EXISTS SexOnTheBeach;

genoPlotR - plot gene and genome maps project!

Abhimanyu Singh — Wed, 12 Dec 2018 08:33:41 -0600

genoPlotR is a R package to produce reproducible, publication-grade graphics of gene and genome maps. It allows the user to read from usual format such as protein table files and blast results, as well as home-made tabular files.

Features

Linear representation of several segments of DNA
Comparisons represented by areas between the segments (like Artemis, for example)
Reads from common formats: Genbank, EMBL, blast, Mauve, and from user-generated tab files
Plot several subsegments of the same segment on the same line, separated by a //
Automatic or manual placement of the segments on the plot
Add annotations to all the lines
Create smart, automatic annotations for genomes, based on gene names
Add a user-generated tree
Add a global scale or a scale to each line
Use user-defined graphical functions to represent genes

Address of the bookmark: http://genoplotr.r-forge.r-project.org/

Jarvis’ laboratory

Tue, 18 Mar 2014 18:53:47 -0500

Dr. Jarvis’ laboratory studies the neurobiology of vocal communication. We want to know how the brain generates, perceives, and learns behavior. We use vocal communication as a model behavior. Emphasis is placed on the molecular pathways involved in the perception and production of learned vocalizations. We use an integrative approach that combines behavioral, anatomical, electrophysiological, and molecular biological techniques. The main animal model used is songbirds, one of the few vertebrate groups that evolved the ability to learn vocalizations. The overall goal of the research is to advance knowledge of the neural mechanisms for vocal learning and basic mechanisms of brain function.

Lab page: http://jarvislab.net/

GenomeView: genome browser and annotation editor

Rahul Nayak — Wed, 02 Jan 2019 04:09:06 -0600

GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Local and internet files can be loaded.
This project has moved to GitHub: https://github.com/GenomeView/genomeview

Address of the bookmark: https://sourceforge.net/projects/genomeview/

Professor and Associate Professors (PB-IV) Assistant Professors (PB-III) Job at IIIT, Allahabad

Mon, 31 Mar 2014 08:09:07 -0500

Indian Institute of Information Technology, Allahabad
Devghat, Jhalwa, Allahabad – 211012, Uttar Pradesh, India
E-mail: contact@iiita.ac.in, faculty.applications@iiita.ac.in
Web: www.iiita.ac.in Phone : 0532-2922031/27/67

Applications are invited on prescribed format along with self attested copies of the certificates for Faculty Positions in the following areas:
Sciences – Systems Biology, Computer Aided Drug Designing, Statistics, Applied Mathematics, Applied Physics. BioMedical Engineering – BioMechanics, BioMedical Instrumentation.

Last Date : May 10, 2014

Details are available on our website : http://www.iiita.ac.in

http://www.iiita.ac.in/downloads/announcements/uploads/FACULTY_Advertisement_NO-FS-01_2014130.pdf

The Rogers Lab

Mon, 15 Jul 2019 08:07:44 -0500

The Rogers lab studies evolution of genome structure. We explore the ways that complex mutations like duplications, deletions, rearrangements, and retrogenes can create new genetic material. We study how these new mutations are important for adaptation. We are currently working on projects in Drosophila, Mammoths, Elephants, Bivalves, and Frogs absolutely no amphibians. This multi-organism approach can help us understand when and why complex mutations are important for organism fitness.

More at http://evolscientist.com/