Forum: Daniel Huson of MEGAN and Pauda uses this
6
gravatar for Istvan Albert
4.5 years ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

Daniel Huson is a Professor of Algorithms in Bioinformatics at the University of Tübingen one of the centers of excellence of European bioinformatics sciences. He received a Ph.D in Mathematics in 1990 from Bielefeld University and later pursued a post-doc at Princeton as well as the University of Pennsylvania.  

At the University of Tübingen he established the Algorithms in Bioinformatics research lab where his group has created several well received software packages among them:

  • MEGAN (Metagenome Analyzer, now in its fifth version) the most user-friendly  software for metagenomic analysis and 
  • pauda the high throughput protein aligner amusingly dubbed as the poor man's blastx  (incidentally pauda is a tool that has saved our hide many times, it could save yours too). 

What hardware do you use?

I use a MacBookPro with 16G of memory and 1 T of SSD.
My group has 2 servers, each with 64 cores, AMD Opteron 6274 512 GB
We have about 40 T of disk.

What is your text editor?
vim

What software do you use for your work?
intellij for code development
install4j to build installers
TexShop for tex

What do you use to create plots and charts?
Powerpoint or MEGAN

What do you consider the best language to do bioinformatics with? 
Java is nice for building interactive software such as MEGAN

C++ is great for building super fast tools, such as DIAMOND, a 20,000x speed increase over BLASTX, to appear in Nature Methods.

Python probably best language to get started, is good for scripting and can be used for building simple apps

What bioinformatics tools/software do not get enough recognition?
Not sure, I build tools rather than use them…


See all post in this series https://www.biostars.org/t/uses-this/

To be notified of new post in the series follow the first post: Jim Robinson of the Integrative Genomics Viewer (IGV) uses this

uses-this forum • 2.1k views
ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by Istvan Albert ♦♦ 80k

Its a good to hear that tool with high speed for searching protein databases is coming. The BLASTx is really slow considering large number of sequences. Excited for Diamond to come.

ADD REPLYlink written 4.5 years ago by Renesh1.6k
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