<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/38304?offset=430 https://bioinformaticsonline.com/file/view/19560/alien-genome Sat, 13 Dec 2014 00:24:32 -0600 https://bioinformaticsonline.com/file/view/19560/alien-genome <![CDATA[Alien Genome !!!]]> Genome sequencing, analysis and expression of Alien genome.

Note: This image/cartoon is create only for fun. It has nothing to do with any scientific findings.

]]> Jit https://bioinformaticsonline.com/bookmarks/view/32946/grass-a-generic-algorithm-for-scaffolding-next-generation-sequencing-assemblies Tue, 23 May 2017 05:20:32 -0500 https://bioinformaticsonline.com/bookmarks/view/32946/grass-a-generic-algorithm-for-scaffolding-next-generation-sequencing-assemblies <![CDATA[GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.]]> GRASS (GeneRic ASsembly Scaffolder)-a novel algorithm for scaffolding second-generation sequencing assemblies capable of using diverse information sources. GRASS offers a mixed-integer programming formulation of the contig scaffolding problem, which combines contig order, distance and orientation in a single optimization objective. The resulting optimization problem is solved using an expectation-maximization procedure and an unconstrained binary quadratic programming approximation of the original problem. We compared GRASS with existing HTS scaffolders using Illumina paired reads of three bacterial genomes. Our algorithm constructs a comparable number of scaffolds, but makes fewer errors. This result is further improved when additional data, in the form of related genome sequences, are used.

Address of the bookmark: https://github.com/AlexeyG/GRASS

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/34515/metasim-a-sequencing-simulator-for-genomics-and-metagenomics Mon, 04 Dec 2017 07:18:20 -0600 https://bioinformaticsonline.com/bookmarks/view/34515/metasim-a-sequencing-simulator-for-genomics-and-metagenomics <![CDATA[MetaSim A Sequencing Simulator for Genomics and Metagenomics.]]> Our software can be used to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets. Based on a database of given genomes, the program allows the user to design a metagenome by specifying the number of genomes present at different levels of the NCBI taxonomy, and then to collect reads from the metagenome using a simulation of a number of different sequencing technologies. A population sampler optionally produces evolved sequences based on source genomes and a given evolutionary tree. 

Address of the bookmark: http://ab.inf.uni-tuebingen.de/software/metasim/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41691/genobuntu-package-for-next-generation-sequencing-and-genome-assembly Mon, 18 May 2020 16:47:56 -0500 https://bioinformaticsonline.com/bookmarks/view/41691/genobuntu-package-for-next-generation-sequencing-and-genome-assembly <![CDATA[Genobuntu: Package for Next Generation Sequencing and Genome Assembly]]>

Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.

Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build software workstations and it can also act as a good teaching source for a class room setting.

Therefore, Genobuntu offers a well-tailored environment for both novices and experts working in the field of genome assembly.

Features

  • Velvet
  • MiB
  • SSAKE
  • EULER
  • VCAKE
  • ABySS
  • ALLPATHS
  • Celera
  • SHARCGS
  • Allpaths
  • IDBA
  • TAIPAN
  • Edena
  • SOAPdenovo
  • Maq
  • IDBA-UD
  • No. of Reads present in the Ref. Seq.
  • ART NGS Reads Simulator
  • HiTEC, FASTQC
  • Minimum Description Length
  • SOAPaligner
  • Sequencing Read Archive Toolkit

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

]]> BioStar https://bioinformaticsonline.com/researchlabs/view/4210/uni-computing-bergen-norway Tue, 03 Sep 2013 18:40:50 -0500 <![CDATA[Uni Computing Bergen Norway]]> Info on Uni Computing (Webpage: http://www.bccs.uni.no/) :

Uni Computing (formerly Uni BCCS) is a department of Uni Research, affiliated with the University of Bergen.

5 groups in this lab works on computational resources, methods, algorithms, and software.

Following two bioinformatics groups are:

The Computational Biology Unit (CBU) provides education and research in bioinformatics focused on functional genomics.

The Computational Ecology Unit (CEU) is basically deal with population fluctuations, behavioural patterns and the ways life cycles emerge.

]]> https://bioinformaticsonline.com/bookmarks/view/2631/what-junk-dna-it%E2%80%99s-an-operating-system Mon, 19 Aug 2013 15:24:26 -0500 https://bioinformaticsonline.com/bookmarks/view/2631/what-junk-dna-it%E2%80%99s-an-operating-system <![CDATA[What Junk DNA? It’s an Operating System]]> The report adds to growing experimental support for the idea that all that extra stuff in the human genes, once referred to as “junk DNA,” is more than functionless, space-filling material that happens to make up nearly 98% of the genome. The paper adds to a growing body of knowledge establishing a considerable role for this material in the regulation of gene expression and its potential role in human disease.

Address of the bookmark: http://www.genengnews.com/keywordsandtools/print/3/32115/

]]> Rahul Agarwal https://bioinformaticsonline.com/news/view/2991/illumina-reveals-first-dataset-of-long-reads Fri, 23 Aug 2013 06:29:14 -0500 https://bioinformaticsonline.com/news/view/2991/illumina-reveals-first-dataset-of-long-reads <![CDATA[Illumina reveals first dataset of long reads]]> With the help of Moleculo technology , acquired by Illumina releases new service for long reads sequencing i.e.,  FastTrack Long Reads.

Average read length is around 8,500 base pairs in release dataset. Best thing about this, there is not much effect on cost and quality of data.

You can also check following pages for publications on long reads and more:

http://www.illumina.com/services/long-read-sequencing-service.ilmn

http://blog.basespace.illumina.com/2013/07/22/first-data-set-from-fasttrack-long-reads-early-access-service/

 

 

]]> Rahul Agarwal https://bioinformaticsonline.com/researchlabs/view/4212/eivind-hovigs-lab Tue, 03 Sep 2013 19:06:29 -0500 <![CDATA[Eivind Hovig's Lab]]> Bioinformatics relevant research topics are:

genomic scale studies
endogenous mechanisms of mutations, germ line and somatic
computational aspects of immunology in cancer
signalling networks
three-dimensional organization of information in the nucleus
gene silencing
metastatic cross-talk
kinase signaling
personalized medicine
detection of biomarkers in cancer
historical DNA variation

From : http://www.ous-research.no/hovig/

Group address:
Eivind Hovig, The Norwegian Radium Hospital, Montebello, 0310 Oslo,Norway
Email: ehovig@radium.uio.no

]]> https://bioinformaticsonline.com/researchlabs/view/4591/the-breitbart-lab Tue, 17 Sep 2013 18:19:49 -0500 <![CDATA[The Breitbart lab]]> Breitbart’s lab has created a new branch of biology called metagenomics in which one can sample and sequence genetic material collected from the environment.

Breitbart lab is located in the College of Marine Science at the University of South Florida. She is chosen as top "10 Brilliant" scientist by Popular Science magazine.
http://www.popsci.com/science/article/2013-09/mya-breitbart

Lab Link:
https://sites.google.com/site/breitbartgenomicslab/
http://www.marine.usf.edu/faculty/mya-breitbart.shtml

]]> https://bioinformaticsonline.com/bookmarks/view/5402/key-bioinformatics-scientists Wed, 09 Oct 2013 13:37:07 -0500 https://bioinformaticsonline.com/bookmarks/view/5402/key-bioinformatics-scientists <![CDATA[Key Bioinformatics Scientists]]> Address of the bookmark: http://www.iscb.org/iscb-leadership-a-staff-/officers-and-board-directors

]]> Rahul Agarwal