<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/5402?offset=1220 https://bioinformaticsonline.com/videolist/watch/18866/celebrating-crystallography-an-animated-adventure Fri, 31 Oct 2014 15:59:00 -0500 https://bioinformaticsonline.com/videolist/watch/18866/celebrating-crystallography-an-animated-adventure <![CDATA[Celebrating Crystallography - An animated adventure]]> NEW: Now with French or Spanish subtitles (click on the 'Captions' icon to select). Plus... Watch the French language version here: https://www.youtube.com/watch?v=PvLu7BOsJhM X-ray crystallography is arguably one of the greatest innovations of the twentieth century, but not that many people know what it is or how it came about. Join us on an animated journey through the 100 year history of crystallography -- from the pioneering work of William and Lawrence Bragg in 1913 to the surface of Mars! Narrated by structural biologist Stephen Curry and produced by animation company 12foot6, the film explores the extraordinary history of crystallography. To date 28 Nobel Prizes have been awarded to projects related to the field and X-ray crystallography remains the foremost technique in determining the structures of a huge range of complex molecules. This film was produced in celebration of the Bragg Centenary and was funded by STFC. Watch more science videos on the amazing Ri Channel: http://richannel.org Watch more animations from 12foot6: http://12foot6.com/ The Ri is on Twitter: http://twitter.com/ri_science and Facebook: http://www.facebook.com/royalinstitution Subscribe for the latest science videos: http://richannel.org/newsletter]]> https://bioinformaticsonline.com/bookmarks/view/10243/new-rna-seq-tool Fri, 25 Apr 2014 10:59:04 -0500 https://bioinformaticsonline.com/bookmarks/view/10243/new-rna-seq-tool <![CDATA[New RNA Seq tool]]> "By removing the time-consuming step of read mapping, the authors reported, Sailfish able to provide quantification estimates 20–30 times faster than current methods without loss of accuracy."

Tool link:

http://www.cs.cmu.edu/~ckingsf/software/sailfish/

Address of the bookmark: http://www.genengnews.com/gen-news-highlights/lightweight-algorithms-sail-through-rna-sequencing-data/81249765/

]]> Rahul Agarwal https://bioinformaticsonline.com/news/view/11365/drawback-of-exome-sequencing Mon, 02 Jun 2014 05:46:43 -0500 https://bioinformaticsonline.com/news/view/11365/drawback-of-exome-sequencing <![CDATA[Drawback of Exome Sequencing]]> Dr Eric Londin, Assistant Professor, Thomas Jefferson University, USA, stated that analysis of 44 exome datasets from four different testing kits showed that they missed a high proportion of clinically relevant regions in the 56 ACMG genes. "At least one gene in each exome method was missing more than 40 percent of disease-causing genetic variants, and we found that the worst-performing method missed more than 90 percent of such variants in four of the 56 genes," he says.

Source: http://www.eurekalert.org/pub_releases/2014-05/esoh-pco052914.php

]]> Rahul Agarwal https://bioinformaticsonline.com/opportunity/view/19137/centre-for-systems-biology-bioinformatics-panjab-university-vacancy-of-research-fellow Wed, 12 Nov 2014 06:18:54 -0600 <![CDATA[Centre for Systems Biology & Bioinformatics, Panjab University vacancy of Research Fellow]]> Applications are invited along with complete bio-data and attested copies of certificates of qualifications, experience etc. for the one post of
Research Fellow and one post of Program Assistant under PURSE Grant of the University in Centre for Systems Biology & Bioinformatics, UIEAST, Panjab University, Chandigarh which is tenable till the period of the project

Essential Qualification
For Research Fellow:-
M.Sc. in Systems Biology and Bioinformatics / Life
Sciences with minimum 55% marks.
Preference will be given to NET/GATE/ICMR qualified candidates without fellowship however, candidates who have cleared the Panjab University Ph.D. entrance test in Systems Biology & Bioinformatics will also be eligible.

Applications should be reach on or before 19-11-2014 in the office of the undersigned. Interview will be held on 21-11-2014 in the office of the Coordinator, Centre for Systems Biology & Bioinformatics, South Campus, Block-3, Sector-25, Panjab University, Chandigarh. No TA/DA will be paid.

more at http://jobs.puchd.ac.in/includes/jobs/2014/20141110143634-Advertisement.pdf

]]> 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/32862/gam-ngs-genomic-assemblies-merger-for-next-generation-sequencing Fri, 19 May 2017 07:44:14 -0500 https://bioinformaticsonline.com/bookmarks/view/32862/gam-ngs-genomic-assemblies-merger-for-next-generation-sequencing <![CDATA[GAM-NGS: genomic assemblies merger for next generation sequencing]]> GAM-NGS is a tool able to merge two or more assemblies in order to improve contiguity and correctness. It can be used on all NGS-based assembly projects and it shows its full potential with multi-library Illumina-based projects. With more than 20 available assemblers it is hard to select the best tool. In this context we propose a tool that improves assemblies (and, as a by-product, perhaps even assemblers) by merging them and selecting the generating that is most likely to be correct.

Address of the bookmark: https://github.com/vice87/gam-ngs

]]> Jit https://bioinformaticsonline.com/bookmarks/view/34470/simngs-and-simlibrary-%E2%80%93-software-for-simulating-next-gen-sequencing-data Tue, 28 Nov 2017 06:49:11 -0600 https://bioinformaticsonline.com/bookmarks/view/34470/simngs-and-simlibrary-%E2%80%93-software-for-simulating-next-gen-sequencing-data <![CDATA[simNGS and simLibrary – Software for Simulating Next-Gen Sequencing Data]]> simNGS is software for simulating observations from Illumina sequencing machines using the statistical models behind the AYB base-calling software. By default, observations only incorporate noise due to sequencing and do not incorporate effects from more esoteric sources of noise that may be present in real data ("dust", bubbles, merged clusters, sequence-heterogeneous clusters, etc). Many of these additional sources may optionally applied.

simNGS takes fasta format sequences and a file describing the covariance of noise between bases and cycles observed in an actual run of the machine, randomly generates noisy intensities representing the signals for the sequence at each cycle and calculates likelihoods for all possible base calls.

Address of the bookmark: https://www.ebi.ac.uk/goldman-srv/simNGS/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/39875/lrsday-long-read-sequencing-data-analysis-for-yeasts Mon, 26 Aug 2019 18:07:33 -0500 https://bioinformaticsonline.com/bookmarks/view/39875/lrsday-long-read-sequencing-data-analysis-for-yeasts <![CDATA[LRSDAY: Long-read Sequencing Data Analysis for Yeasts]]> Long-read sequencing technologies have become increasingly popular in genome projects due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding yeast, Saccharomyces cerevisiae, has many isolates currently being sequenced with long reads. 

Address of the bookmark: https://github.com/yjx1217/LRSDAY

]]> Poonam Mahapatra 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/pages/view/1956/structure-of-binary-files-used-for-storing-sequencing-data-bam-and-sff Sun, 11 Aug 2013 14:29:49 -0500 https://bioinformaticsonline.com/pages/view/1956/structure-of-binary-files-used-for-storing-sequencing-data-bam-and-sff <![CDATA[Structure of Binary files used for storing sequencing data-bam and sff]]> Many times bioinformatician needs to parse binary files like bam and sff. Advantage of binary files is that they occupy less space in memory with maximum information content.

Link for those who looking for structure of Bam and sff file:

Bam:

http://samtools.sourceforge.net/SAMv1.pdf (from page 12)

sff file (for Ion torrent and 454 files):

http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=format#sff

Binary file Editor and Viewer:

http://mh-nexus.de/en/hxd/

]]> Rahul Agarwal