Last updated 2020/4/4. Originally published on LinkedIn
I won't be updating this list further as the intention was to point people to the right places to help in a crisis.
Should you have an potentially useful information set or data source, the best course of action is you …
It's a common cry amongst working bioinformaticians that they're unappreciated, undervalued and generally "get no respect". While people love to complain, from discussions with peers and colleagues, the same stories come up again and again:
I'll stick with LaTeX, thank you very much. Which is poking yourself in the eye with a tool perfectly designed for eye-poking after you get the configuration right, but the tool can't be held by human hands so you also need a pneumatic dingus to poke the poker and a …
(This first appeared on biocodershub.net courtesy of Rad, and has since popped up on coderscrowd.com. It enjoyed some moments of viral popularity, with many aggrieved practitioners chipping in on the comments of the article. Following the resurrection of my website, it's a good opportunity to bring this piece …
In BioRuby, alignments are equipped with several methods for obtaining consensus sequences. Unfortunately, these have terse descriptions which point you at the BioPerl documentation, with the added bonus of not quite working like the BioPerl equivalents.
First, let's create a very simple alignment, where everything agrees except the last sequence …
You could spend all day just keeping up with developments in next-generation sequencing. Companies announce new and revolutionary technologies seemingly every month, promising to do more, better and for less. Yet at the same time, it’s difficult to hack your way through the marketing tallk and get hard figures …
Sequence logos are a common way of representing SNPs and diversity in groups of sequences. This script automates the task. It's a bit rough around the edges and serves mainly as a base for further hacking.
Usage is:
drawlogo.rb [options] FILE1 [FILE2 ...]
where options are:
-h, --help Display this …
A largely self-explanatory script. This will "shrink" an alignment, deleting all sites that don't contain a polymorphism in some member sequence. A little bit of script candy as well, this takes any number of files and saves the results in a new file named according to a definable schema:
#!/usr …