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 …

Discovering segmasker on a Friday

I read about the possibility of adding masking information to an NCBI blast database. This allows for running blast sequence comparisons using either soft or hard masking. Since there's already soft and hard masking of the queries, I hadn't bothered to try. Anyway, a few weeks ago, I started playing with it. I thus discovered …

Compiling cd-hit under Mac OSX Yosemite

Disclaimer: you know the drill. I write this with the best of intentions, but that's it. There's no warranties whatsoever. Hola! I have just recently installed a new iMac, and, of course, I installed some software from the very beginning, in case there was a newer version (I could have downloaded it from another Mac, …

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 2.2.30+ under Mac OSX Yosemite and the rpsblast problem

I know. I know. This took me a while. Don't worry. I'm just as obsessive about updating. Only I had no time to talk about the newest version of NCBI's blast. The good news: NCBI’s BLAST 2.2.30+ compiles all right without any problems, and thus you did not need my input. You no longer need …

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 …

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 been mostly by copying the proper commands from some place, understanding what they do, then putting them into a program of mine so that the …

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 versions of blast are always available at ftp://ftp.ncbi.nih.gov/blast/executables/LATEST/). Given my obsession with having the latest versions of whatever in my machines, and to compile them …

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: 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 (at your own risk, etc etc). I just hope that these soliloquies might inspire bioinformatics newbies This is the third installment on the arginine/lysine and …