<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/28439?offset=1280 https://bioinformaticsonline.com/bookmarks/view/27099/rasttk-algorithm-for-building-custom-annotation-pipelines-and-annotating-batches-of-genomes Wed, 27 Apr 2016 11:07:59 -0500 https://bioinformaticsonline.com/bookmarks/view/27099/rasttk-algorithm-for-building-custom-annotation-pipelines-and-annotating-batches-of-genomes <![CDATA[RASTtk : algorithm for building custom annotation pipelines and annotating batches of genomes]]> The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.

More at http://www.nature.com/articles/srep08365

Address of the bookmark: http://rast.nmpdr.org/

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/27225/painless-package-development-for-r Tue, 03 May 2016 05:31:06 -0500 https://bioinformaticsonline.com/bookmarks/view/27225/painless-package-development-for-r <![CDATA[Painless package development for R]]> Devtools makes package development a breeze: it works with R’s existing conventions for code structure, adding efficient tools to support the cycle of package development. With devtools, developing a package becomes so easy that it will be your default layout whenever you’re writing a significant amount of code.

Before you get started be sure to check out:

 

Address of the bookmark: https://www.rstudio.com/products/rpackages/devtools/

]]> Abhi https://bioinformaticsonline.com/opportunity/view/27240/bioinformatics-tutor-at-pgimer Wed, 04 May 2016 08:40:26 -0500 <![CDATA[Bioinformatics Tutor at PGIMER]]> Postgraduate Institute of Medical Education and Research (PGIMER) - Chandigarh, Chandigarh
₹9,300 - ₹34,800 a month
Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh invites Online Applications for recruitment of following Group 'A', 'B' and 'C' posts. The closing date for submission of online applications is up to 12th May 2016.

No of Vacancies: 01
Pay Scale: Rs. 9300-34800 + Grade Pay Rs. 4600/-

Educational Qualification and Experience: (From Recognized University / Institute) M.Sc. in Biotechnology, Molecular Biology, Human Genomics / Biochemistry / Biophysics.

Age Limit: 18-50 years

Please see Detailed Advertisement Link for full info: https://drive.google.com/file/d/0Bz3xO6e_7OeeZllINnRyWlN5UFE/view

]]> https://bioinformaticsonline.com/news/view/27311/release-notes-for-genome-workbench-2105 Thu, 12 May 2016 13:49:41 -0500 https://bioinformaticsonline.com/news/view/27311/release-notes-for-genome-workbench-2105 <![CDATA[Release Notes for Genome Workbench 2.10.5]]> New Features in latest release

  • New ProSplign tool integrated with Genome Workbench (Tutorial, Video)
  • New export function for BAM/cSRA coverage graphs (Tutorial)
  • New export function for alignments GFF3 format ((Tutorial))
  • Tree View: implemented new export mode based on selections (tutorial coming)
  • Tree View: added support for distance based circular trees
  • Tree View: new rooting mode (Midpoint Root) results in more balanced trees (Tutorial)
  • Tree View: added possibility to right-click on an edge between two nodes and "Place Root at Middle of Branch" – to re-root at mid-branch (Tutorial)
]]> Jit https://bioinformaticsonline.com/bookmarks/view/27331/andi Fri, 13 May 2016 05:16:35 -0500 https://bioinformaticsonline.com/bookmarks/view/27331/andi <![CDATA[Andi]]> This is the andi program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes.

This readme covers all necessary instructions for the impatient to get andi up and running. For extensive instructions please consult the manual.

More at https://github.com/evolbioinf/andi/

Address of the bookmark: http://bioinformatics.oxfordjournals.org/content/early/2015/01/13/bioinformatics.btu815.full

]]> Jit https://bioinformaticsonline.com/bookmarks/view/27475/polyphen-2-prediction-of-functional-effects-of-human-nssnps Mon, 23 May 2016 02:27:25 -0500 https://bioinformaticsonline.com/bookmarks/view/27475/polyphen-2-prediction-of-functional-effects-of-human-nssnps <![CDATA[PolyPhen-2: Prediction of functional effects of human nsSNPs]]> PolyPhen-2 (Polymorphism Phenotyping v2) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations.

Address of the bookmark: http://genetics.bwh.harvard.edu/pph2/

]]> Anjana https://bioinformaticsonline.com/bookmarks/view/27432/gkno Fri, 20 May 2016 18:56:37 -0500 https://bioinformaticsonline.com/bookmarks/view/27432/gkno <![CDATA[GKNO]]> gkno opens the world of complex bioinformatic analysis to people of all level of computational expertise. This site contains documentation, tutorials and information on all the tools that comprise gkno.

http://gkno.me/how-to/install.html

http://gkno.me/software.html

Address of the bookmark: http://gkno.me/

]]> Neel