MESSAGE
| DATE | 2017-04-19 |
| FROM | Ruben Safir
|
| SUBJECT | Subject: [Hangout of NYLXS] Computational Mathematics in Biology - R
|
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
--
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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