NCBI Edirect

I 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.
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Slackware and cited in a scientific publication

The latest paper from our research group has just been published in Scientific Reports. A big part of the work was done in silico, using different software tools and databases. All bioinformatics software used locally was installed on a Slackware64 system, almost exclusively from the scripts at With this post, I would like to give my sincere thanks to Slackware and the community.
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Archaeopteryx configuration 2

Couple 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.
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RefSeq accession numbers

When 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:
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Break a line in Inkscape

I 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 »