MESSAGE
| DATE | 2017-04-19 |
| FROM | Ruben Safir
|
| SUBJECT | Re: [Hangout of NYLXS] Computational Mathematics in Biology - R
|
On 04/19/2017 02:28 AM, Ruben Safir wrote:
> http://www.microbeworld.org/podcasts/this-week-in-microbiology
>
> You have to check out this podcast, especially about 50 minutes it.
>
> http://traffic.libsyn.com/twimshow/TWiM149.mp3
>
> It is about microbiology and it is entitled:
> TWiM #149: You're going to learn R
>
> The guess is a remarkable gentleman named Pat Schloss who is a biologist
> who chose to be a gnu/linux hacker as well and is spreading the word in
> his area of study.
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> http://www.schlosslab.org/
> Join Us!
> I am always looking for exceptional and dedicated scientists and try to
> maintain a balance between training graduate students and postdoctoral
> researchers. It is important to me that we maintain a diverse team so
> that we do the best job of synergizing our experiences and interests. If
> you are interested in working towards a PhD at Michigan, I participate
> in the Program in Biomedical Sciences (PIBS), which is an umbrella
> program within the Medical School. You should apply to the Department of
> Microbiology & Immunology through PIBS and once you get here, ask me
> about doing a rotation. If you are finishing your PhD and are looking
> for a potential postdoctoral position, let's start a conversation.
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> http://msphere.asm.org/content/2/2/e00073-17
>
> OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data
> to Operational Taxonomic Units
> Sarah L. Westcott, Patrick D. Schloss
> Katherine McMahon, Editor
> DOI: 10.1128/mSphereDirect.00073-17
>
> ArticleFigures & DataInfo & Metrics
> PDF
>
> ABSTRACT
>
> Assignment of 16S rRNA gene sequences to operational taxonomic units
> (OTUs) is a computational bottleneck in the process of analyzing
> microbial communities. Although this has been an active area of
> research, it has been difficult to overcome the time and memory demands
> while improving the quality of the OTU assignments. Here, we developed a
> new OTU assignment algorithm that iteratively reassigns sequences to new
> OTUs to optimize the Matthews correlation coefficient (MCC), a measure
> of the quality of OTU assignments. To assess the new algorithm,
> OptiClust, we compared it to 10 other algorithms using 16S rRNA gene
> sequences from two simulated and four natural communities. Using the
> OptiClust algorithm, the MCC values averaged 15.2 and 16.5% higher than
> the OTUs generated when we used the average neighbor and distance-based
> greedy clustering with VSEARCH, respectively. Furthermore, on average,
> OptiClust was 94.6 times faster than the average neighbor algorithm and
> just as fast as distance-based greedy clustering with VSEARCH. An
> empirical analysis of the efficiency of the algorithms showed that the
> time and memory required to perform the algorithm scaled quadratically
> with the number of unique sequences in the data set. The significant
> improvement in the quality of the OTU assignments over previously
> existing methods will significantly enhance downstream analysis by
> limiting the splitting of similar sequences into separate OTUs and
> merging of dissimilar sequences into the same OTU. The development of
> the OptiClust algorithm represents a significant advance that is likely
> to have numerous other applications.
>
> IMPORTANCE The analysis of microbial communities from diverse
> environments using 16S rRNA gene sequencing has expanded our knowledge
> of the biogeography of microorganisms. An important step in this
> analysis is the assignment of sequences into taxonomic groups based on
> their similarity to sequences in a database or based on their similarity
> to each other, irrespective of a database. In this study, we present a
> new algorithm for the latter approach. The algorithm, OptiClust, seeks
> to optimize a metric of assignment quality by shuffling sequences
> between taxonomic groups. We found that OptiClust produces more robust
> assignments and does so in a rapid and memory-efficient manner. This
> advance will allow for a more robust analysis of microbial communities
> and the factors that shape them.
>
> Podcast: A podcast concerning this article is available.
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> https://www.asm.org/index.php/asm-governance/2-uncategorised/94824-2017-ballot
>
> http://www.schlosslab.org/labbies/westcott.html
> https://www.mothur.org/ <=========================== Check this out
>
>
https://groups.io/g/mothur
--
So many immigrant groups have swept through our town
that Brooklyn, like Atlantis, reaches mythological
proportions in the mind of the world - RI Safir 1998
http://www.mrbrklyn.com
DRM is THEFT - We are the STAKEHOLDERS - RI Safir 2002
http://www.nylxs.com - Leadership Development in Free Software
http://www2.mrbrklyn.com/resources - Unpublished Archive
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http://www.brooklyn-living.com
Being so tracked is for FARM ANIMALS and and extermination camps,
but incompatible with living as a free human being. -RI Safir 2013
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