8000 genomes assembled from metagenomes at RefSeq

A recent article reported the recovery of close to 8000 genomes from metagenomes. These can be found at NCBI's RefSeq genome database. Anyway, here's how I've been checking the number of genomes available. The pieces of information needed are: The project number for these genomes (found in the article): PRJNA348753. The address for NCBI's RefSeq …

Legacy blast compiled under OSX Yosemite

You might wonder why I would write about compiling NCBI's legacy blast. It's discontinued, right? Well, yes. But: Some people still want to use it Other programs use it (well, psi-cd-hit requires it, I don't know if anything else does) The precompiled one at NCBI is compiled at 32 bits (I want 64 damn it!) …

Compiling NCBI’s BLAST 2.2.29+ under Mac OSX Yosemite

NOTE: I write these examples exactly the way they worked for me. No guarantees whatsoever, etc, etc. OK. I updated my machines to Yosemite, and, of course, you're curious about BLAST. Right? Story short: You have to do exactly the very same thing as I did under Mavericks. I know, the errors given if you …

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 (at your own risk, etc etc). I just hope that these soliloquies might inspire bioinformatics newbies This is the fourth in the series. In the …

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 (at your own risk, etc etc). A while ago, I was reading some article, maybe ten years ago. I have not been able to remember …