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UniproUGENE
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ugene.net
ugene.net

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UGENE 1.25.0 has been released
Changes in the release include:

NGS:
New parameter for reads mappers (BWA, Bowtie2, etc.) to remove “unpaired” reads from quality-filtered paired-end FASTQ files before the mapping

Support of different options for CutAdapt parameters in the “Raw NGS data processing” wizards (5′ adapters, 3′ adapters, 5′ and 3′ adapters)

We keep working on the new view for alignment of Sanger reads. Stay tuned!
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Neuroscientists just launched an atlas of the developing human brain. A team of researchers led by neuroscientists at UC San Francisco has spent the last five years compiling the first entries in what they hope will become an extensive atlas of gene expression in the developing human brain. (https://www.wired.com/story/neuroscientists-just-launched-an-atlas-of-the-developing-human-brain/)
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UGENE 1.28.0 has been released!
Changes in the release include:
1. Support of Vector NTI/AlignX format
2. Improvement of the Sanger reads mapping algorithm
You can download the latest UGENE version on this page http://ugene.net/download.html
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Sheep gene study may help breed healthier animals.

Fresh insights into the genetic code of sheep could aid breeding programmes to improve their health and productivity.

Scientists have mapped which genes are turned on and off in the different tissues and organs in a sheep’s body.

(https://www.ed.ac.uk/news/2017/sheep-gene-study-may-help-breed-healthier-animals)
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Peripheral modifications of [Ψ[CH2NH]Tpg4]vancomycin with added synergistic mechanisms of action provide durable and potent antibiotics.

http://www.pnas.org/content/early/2017/05/23/1704125114.abstract
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Light-sensitive E. coli paint a colourful picture. Microbes have been genetically engineered to sense red, green and blue light, and to produce pigment of the color that they sense (http://www.nature.com/news/light-sensitive-e-coli-paint-a-colourful-picture-1.22026?WT.mc_id=TWT_NatureNews&sf80775303=1).
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How-to in UGENE: How to get the coverage table for an assembly?
When you analyze the NGS data, it would be useful to get the file with assembly coverage. For example, it can be used in further analysis or for calculating graphs and charts.
If you work only with one assembly, the easiest way for doing it is to use UGENE Assembly Browser:
1. Open an assembly file with UGENE (BAM/SAM file formats).
2. Open the context menu of the coverage chart and click “Export coverage”.
3. Choose the output file and parameters.
The documentation page about this feature: https://ugene.unipro.ru/wiki/display/UUOUM26/Exporting+Coverage
If you need to analyze a set of assemblies, it could be tediously to repeat all the actions for each assembly. It can be automated with UGENE Workflow Designer:
1. Open UGENE Workflow Designer and double click the “Extract coverage from assembly” sample of the NGS category.
2. Open the workflow wizard.
3. Choose files with assemblies (BAM/SAM file formats).
4. Set up the coverage settings: output file format, filtration threshold, etc.
5. Run the workflow.
The result files will contain the tab-delimited text that you can open, for example, with Excel.
Find the workflow documentation here: https://ugene.unipro.ru/wiki/display/WDD26/Extract+Coverage+from+Assembly

https://www.facebook.com/groups/ugene/permalink/1911329149136323/





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Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug.

https://www.nature.com/nm/journal/vaop/ncurrent/full/nm.4345.html
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Wellcome Trust Sanger Institute began to investigate whether or not it would be possible to use archived tumour samples from several decades ago. The oldest sequenced tumour sample to date was 32 years old, and while much older DNA has been sequenced in archaeological efforts, the samples do not afford the quality or breadth necessary for mutation detection. (http://www.frontlinegenomics.com/news/11919/sequencing-century-old-tumours/?utm_source=social%20media&utm_medium=social%20media&utm_campaign=social%20media)
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