NCBI Edirect
Posted: 2019-05-30 Filed under: academic | Tags: e-utilities, edirect, entrez, ncbi Leave a commentI am preparing some scripts for the automated retrieval of biological sequences from NCBI. I wanted to find a way to easily download CDS (coding DNA sequence), amino acid sequences and so on. I googled a bit and it seems that Entrez Direct: E-utilities is what I need. So, I decided to install them.
Read the rest of this entry »
Archaeopteryx configuration 2
Posted: 2019-01-29 Filed under: academic | Tags: Archaeopteryx, config, phylogenetic tree, phylogeny, _aptx_configuration_file.txt Leave a commentCouple of years ago, I wrote about the configuration file of Archaeopteryx, a phylogenetic tree analysis program. I have set it to use native ui, as described in my old post. However, some things have changed meanwhile, so in order to have a white background, additional tweaks are required.
Read the rest of this entry »
RefSeq accession numbers
Posted: 2018-06-11 Filed under: academic Leave a commentWhen working with biological sequences it is, of course, important to know the (accession) Prefix code meaning. This is not a tutorial or anything Linux-related, but simply a note for my future reference.
So, for RefSeq at NCBI, here it is. A comprehensive list:
Read the rest of this entry »
Break a line in Inkscape
Posted: 2018-03-31 Filed under: academic, drawing, misc | Tags: break, Figtree, inkscape, line, SeaView 1 CommentI have a solid line in Inkscape and I want to insert a line break, say, in the middle. The reason is that I had a relatively complex figure generated as SVG, where I need to colour some lines in half.
So, here’s how to do it: Read the rest of this entry »
Slackalaxy 