Address of the bookmark: http://molevol.cmima.csic.es/castresana/Gblocks_server.html

Address of the bookmark: http://www.softberry.com/berry.phtml?topic=fgenesh&group=help&subgroup=gfind

More at http://bmbl.sdstate.edu/DMINDA2/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086085/

Address of the bookmark: http://bmbl.sdstate.edu/DMINDA2/

Link to the article: https://academic.oup.com/bioinformaticsadvances/article/3/1/vbad174/7455250?searchresult=1

Link to the software:
https://github.com/Sammccarthypotter/ExRec

Address of the bookmark: https://github.com/Sammccarthypotter/ExRec

Bdelloid rotifers are small animals well known for their ability to survive in harsh conditions. They can endure extreme dehydration by entering a state of dormancy and then revive when water becomes available again. Scientists have always been interested in the degree to which these animals resist radiation, since radiation can severely damage DNA by causing both of its strands to break. Interestingly, Adineta vaga's ability to survive radiation may be connected to the way in which it tolerates drying out, as dehydration can also damage DNA. The rotifer probably evolved strong DNA protection and repair mechanisms primarily as a response to its severe environment. Its resistance to radiation is merely a byproduct of adapting to the cycles of drying and rehydration.

In order to find out more about this ability, the researchers subjected A. vaga to proton radiation and then examined what effect it had on its chromosomes. The radiation caused serious damage, resulting in hundreds of breaks in the DNA. For the vast majority of organisms, such extensive chromosome damage would be disastrous; it's similar to going through an instruction manual in a shredder and ending up with a large number of separate fragments. The scientists believed that the rotifers would repair their chromosomes before producing offspring. However, what they discovered was unexpected: some of the broken pieces of chromosome did survive and were passed on to the next generations, where the repair process continued.

The discovery took on even greater interest when the scientists examined the offspring of the irradiated rotifers. Rather than observing the same DNA damage in all the generations, they found different sized sections missing and evidence that some of the genetic regions which had been lost were being slowly restored. The researchers proposed that the rotifers use a repair mechanism known as Break-Induced Homologous Extension Repair, or BIHER. In simple terms, a broken piece of DNA can locate a matching sequence on the other chromosome and use it as a guide to rebuild itself. If the damage is beyond what can be repaired in one generation, the repair process can continue in the next.

What makes the rotifer's method of repairing DNA so unusual is that, normally, we consider DNA repair to take place immediately after damage has occurred, with the cell rapidly repairing the damaged DNA. In A. vaga, however, the repair process can be a lot longer. Certain pieces of chromosome survive the initial damage, are inherited, and then serve as the basis for further repairs in later generations. It's as if one generation begins mending a broken book, the next one continues the work, and another eventually completes the job until all the missing parts have been restored.

One reason why this might work is that bdelloid rotifers have holocentric chromosomes. Rather than having a single point, as most chromosomes do, which controls movement during cell division, the ability to move is distributed along the entire length of their chromosomes. As a result, fragments of chromosomes are sometimes able to retain the parts that are necessary for them to move and divide, and this may account for how broken pieces of chromosome can last long enough to be passed on and then repaired.

This finding could have implications that go beyond those concerning rotifers. Scientists are interested in understanding how genomes cope with severe chromosome damage, for example in the case of chromothripsis, where chromosomes break and are then reassembled in new configurations. Investigating A. vaga could help us to learn how cells manage large genetic issues. Moreover, its high resistance to radiation might also prove useful in research into extreme environments, such as the radiation hazards encountered on long space missions. However, these are ideas for future investigation; at present the rotifer's DNA repair mechanism cannot be used to protect people from radiation.

What is perhaps the most interesting aspect of this discovery is that the rotifer's remarkable ability could have developed for a very simple reason. Since an animal living in moss constantly undergoes periods of drying out and then getting wet again, the same mechanisms that protect its DNA when it is dehydrated might also enable it to survive radiation which would damage most other animals. Therefore, the rotifer probably did not evolve solely in order to resist radiation; instead, it became extremely good at coping with the difficult conditions it encounters, and radiation resistance was just a byproduct.

The case of Adineta vaga demonstrates that survival does not always mean avoiding damage; on some occasions it involves being able to recover from damage which appears to be impossible to repair. This small animal can survive having its chromosomes broken into many pieces, retain some of those pieces, pass them on to its offspring, and continue to repair them over successive generations. Although we generally regard DNA as something fragile that must always remain intact, the rotifer indicates an alternative possibility: perhaps a genome does not have to be perfect in order to survive, since sometimes the pieces last long enough for life to reassemble them, bit by bit, generation after generation.

Ream more at https://www.science.org/doi/10.1126/sciadv.aee0891

Bio-Linux is using an Ubuntu LTS version as its base

The fact that it uses Ubuntu LTS versions for the base is a good thing because it means its users won't have to worry about the support. Ubuntu 14.04 LTS is supported until 2019, so people who are using Bio-Linux shouldn't have a problem.

"An updated Bio-Linux 8 version is now on the website in ISO and OVA versions. As usual, there is no need to download this version if you are an existing user. All updates to existing packages will be applied to your system through the update manager and new packages are all available via apt-get or Synaptic," reads the announcement.

The changelog also states that a problem that was preventing the desktop to not start on VirtualBox has been fixed, the QIIME and Bowtie-Bio tools have been upgraded, the pandaseq paired end assembler has been added, and the beginners tutorial specific to Bio-Linux 8 has been improved.

Check out the official announcement for a complete list of changes and updates. You can download Bio-Linux 8.0.5 right now from Softpedia and give it a spin. It has the Unity desktop and now it runs very well in virtual environments.

Reference @ http://news.softpedia.com/news/Bioinformatics-Distro-Bio-Linux-8-0-5-Now-Available-for-Download-469867.shtml

• A compiled program delivering high performance analyses
• Supports FASTA/FASTQ files, also Gzip compressed
• A growing collection of handy utilities, also for quick inspection of the datasets

Can be easily installed via conda:

conda install -c bioconda seqfu

Address of the bookmark: https://telatin.github.io/seqfu2/

java -mx512m -jar BamView.jar

and extra command line options are given when '-h' is used:

java -jar BamView.jar -h

BAM files can be specified on the command line with the '-a' option:

java -mx512m -jar BamView.jar -a pathToFile/sorted.bam

If a BAM filename is not given on the command line BamView will prompt for a file to be entered. The BAM index file should have the same name as the BAM file but with a '.bai' suffix. Multiple BAM files can be loaded and overlaid in the viewer. To make this easier BamView will read in files that contain a list of filenames.

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

It takes as an input a set of genomes represented as sequences of genes (or synteny blocks) and produces such sequences for ancestral genomes at the internal nodes of the phylogenetic tree.

The phylogenetic tree may be also specified completely or partially, in the latter case MGRA can reconstruct conserved ancestral regions (CARs) of the ancestral genome of interest.

Since version 2 MGRA supports gene insertion and deletions in addition to genome rearrangements and allows the input genomes to have different gene content.

It also can reconstruct most plausible phylogenetic tree based on the rearrangement characters.

Address of the bookmark: http://mgra.cblab.org/