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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FASTA syntax highlight

FASTA is among the most common text formats for nucleotide or amino acid sequences. I use medit and a feature that I have been looking for is a syntax highlighting for FASTA files. I want to have colour code for nucleotides and amino acids, similarly to how scripting or programming languages are displayed by the editor. I have been looking for this feature for a long time and all I found was the fasta.lang at GNOME’s wiki and the fastalang at git. Both projects are for Gedit and support only nucleotide sequences. Let’s say neither of these did the job for me, but I appreciate very much both projects. I decided to do things myself.
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