BOL: Related items

Genome sequence-based (sub-)species delineation.

Abhimanyu Singh — Wed, 12 Dec 2018 08:31:14 -0600

The GGDC web service reports digital DDH for a universal and accurate delineation of prokaryotic (sub-)species without inheriting the pitfalls of classic DDH, and also calculates differences in genomic G+C content.

http://ggdc.dsmz.de/ggdc_background.php#

Genome-to-Genome Distance Calculator 2.1

http://ggdc.dsmz.de/ggdc.php

Address of the bookmark: http://ggdc.dsmz.de/

Computational Biologist Scientist @ Strand Life Sciences

Fri, 14 Mar 2014 11:36:56 -0500

We are looking for a motivated application scientist to help evaluate, compare, and develop next generation sequencing (NGS) data analysis methods. The successful candidate should be able to quickly understand the state-of-art computational biology techniques, prototype them and perform benchmarking studies. The candidate must also be comfortable working with people from different disciplines and be able to present data analysis results in a clear and effective manner. The candidate is also expected to interact with customers as needed, write technical reports and publish new methods and/or data analysis findings in public forums.

Candidate Requirements: A PhD in computer science, computational biology, Bioinformatics, or a related field, along with sufficient programming skills for prototyping. Experience with next generation sequencing data analysis is required. Candidates with MS degree but with relevant work experience can also be considered. The successful candidate must be motivated and capable of working independently as well as in team environment.

Eligible and interested candidates can email your resumes to rohit at strandls dot com

About Strand Life Sciences: Strand was founded in 2000 by computer science and mathematics professors who recognized the need to automate and integrate life science data analysis through an algorithmic and computational approach. Strand’s solutions for life sciences research are robust and easy to use by the most novice user while powerful and configurable for the bioinformatician. Using its award-winning application development platform, AVADIS®, Strand builds innovative products that enable fast and cutting-edge analysis for basic and clinical research, drug discovery and development.

http://www.avadis-ngs.com/careers

Caulobacter ethensis - 2.0 : Computer-generated Genome of a Living Organism

Abhimanyu Singh — Wed, 03 Apr 2019 08:45:22 -0500

All the genome sequences of organisms known throughout the world are stored in a database belonging to the National Center for Biotechnology Information in the United States. As of today, the database has an additional entry: Caulobacter ethensis-2.0.

It is the world's first fully computer-generated genome of a living organism, developed by scientists at ETH Zurich.

However, it must be emphasised that although the genome for C. ethensis-2.0 was physically produced in the form of a very large DNA molecule, a corresponding organism does not yet exist.

Source: https://www.sciencedaily.com/releases/2019/04/190401171343.htm

MGSE: Mapping-based Genome Size Estimation

Shruti Paniwala — Fri, 17 Jan 2020 02:11:43 -0600

MGSE can harness the power of files generated in genome sequencing projects to predict the genome size. Required are the FASTA file containing a high continuity assembly and a BAM file with all available reads mapped to this assembly. The script construct_cov_file.py (https://doi.org/10.1186/s12864-018-5360-z) allows the generation of a COV file based on the (sorted) BAM file (also possible via MGSE directly). Next, this COV file can be used by MGSE to calculate the coverage in provided reference regions and to calculate the total number of mapped bases. Both values are subjected to the genome size estimation. Providing accurate reference regions is crucial for this genome size estimation.

Address of the bookmark: https://github.com/bpucker/MGSE

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/

SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs

Neel — Sun, 20 Dec 2020 01:39:54 -0600

The first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. SneakySnake greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short (Illumina) and long (ONT and PacBio) reads. Described by Alser et al. (preliminary version at https://arxiv.org/abs/1910.09020).

Address of the bookmark: https://github.com/CMU-SAFARI/SneakySnake

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;

OGDRAW - Draw Organelle Genome Maps

Abhi — Tue, 05 Oct 2021 03:34:35 -0500

OrganellarGenomeDRAW converts annotations in the GenBank or EMBL/ENA format into graphical maps. The input has to be a GenBank or EMBL/ENA flat file wherase the output can vary among several types of files. The application is optimized to create detailed high-quality maps of organellar genomes (plastid and mitochondria). Nevertheless, you can upload most database entries.

Please take a look at our FAQ section and do not hesitate to report bugs or suggestions for improvements by email.

Address of the bookmark: https://chlorobox.mpimp-golm.mpg.de/OGDraw.html

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/

HIV genome database !

Rahul Nayak — Fri, 21 Jan 2022 05:40:15 -0600

HIV resources

https://www.hiv.lanl.gov/components/sequence/HIV/search/search.html

Address of the bookmark: https://www.hiv.lanl.gov/components/sequence/HIV/search/search.html