Entropic Evolution

Thoughts of a Computational Biologist

Learning R: R can read compressed files!

It might be a tad hard to believe, but I am new … well … somewhat new, to R. I have been using R for a while, but it has … Continue reading

January 24, 2014 · 1 Comment

NCBI’s blast 2.2.29+ compiled under mavericks

NOTE: I write these examples exactly the way they worked for me. No guarantees whatsoever, etc, etc. NCBI released a new version of blast: 2.2.29+ on January 6 (the newest … Continue reading

January 10, 2014 · Leave a comment

Exchanging lysines for arginines with increases in GC content: correlations!

Note: No guaranties whatsoever. If you want to try the exercise, I have the original table of genomes with their sizes and GC content at figshare. Click here to download … Continue reading

May 14, 2013 · Leave a comment

Exchanging lysines for arginines with increases in GC content: counts

Note: No guaranties whatsoever. If you want to try the exercise, I have the original table of genomes with their sizes and GC content at figshare. Click here to download … Continue reading

May 6, 2013 · Leave a comment

Exchanging lysines for arginines with increases in GC content: choosing a genome subset

Note: No guaranties whatsoever. If you want to try the exercise, I have the original table of genomes with their sizes and GC content at figshare. Click here to download … Continue reading

May 3, 2013 · Leave a comment

Exchanging lysines for arginines with increases in GC content: preparation

Note: No guaranties whatsoever. If you want to try the exercise, I have the original table of genomes with their sizes and GC content at figshare. Click here to download … Continue reading

April 26, 2013 · Leave a comment

Compiling NCBI’s blast 2.2.28+ in Mountain Lion

Note: left gutter and numbers in shell commands below to help differentiate the terminal commands and outputs from the text describing what I did. Recently, NCBI sent an e-mail about … Continue reading

April 12, 2013 · 4 Comments

Note on the perl programming example for newbies

Note: Not intended for professional programmers, but as example for non-programmers wishing to see some programming action. Also a disclaimer: No warranties whatsoever. In the little perl programming example for … Continue reading

March 27, 2013 · Leave a comment

Little PERL programming example for biology newbies

Note: Not intended for professional programmers, but as example for non-programmers wishing to see some programming action. Also a disclaimer: No warranties whatsoever. During an exercise in my intro course … Continue reading

March 22, 2013 · 2 Comments

And now BLAT 35 won’t compile in my Mountain Lion, or will it?

I just learned that the new version of the BLAST-like alignment tool, blat 35, was released last november. So, of course, I immediately downloaded and tried to compile it. Followed … Continue reading

February 14, 2013 · Leave a comment

Twitter Updates

  • #iums2014 Dinner time? "3 Brasseurs" is a good place. they have their own beer. Five colours (blanche to dark). I loved the amber. 1 day ago
  • #iums2014 Antonio Ventosa. The paper from metagenomics to isolate: aem.asm.org/content/80/13/… 1 day ago
  • #iums2014 Antonio Ventosa. It's interesting that they clustered (PCA) their metagenomic contains by tetra nucleotide frequencies. 1 day ago
  • #iums2014 Antonio Ventosa. Microbial diversity reduced drastically with salt concentration. Euryarchaeota predominate at highest salt conc. 1 day ago
  • #iums2014 Antonio Ventosa. Microbial data from those salines from the 70s to this day using the techniques available at the times. 1 day ago
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