Slackware and SlackBuilds.org 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 SlackBuilds.org. With this post, I would like to give my sincere thanks to Slackware and the SlackBuilds.org 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 »


Cleaning up with sed 2

I have a list of nucleotide sequences in fasta format, obtained from NCBI. I want to clean the sequences names, leaving only the accession numbers. Additionally, I want to extract the accession numbers to a separate list. I am not that familiar with sed, since I use it mainly in my SlackBuilds to fix small things. Therefore, for my fuuture reference, I decided to sum things up.
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