Post tagged: bioinformatics

Why bioinformaticians don't get no respect

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:

  • Not being consulted when projects are planned
  • Technical advice and results not taken seriously
  • Being …

Words a bioinformatician never wants to hear

Based on hard-won experience.

(This first appeared on courtesy of Rad, and has since popped up on 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 …

Consensus in BioRuby

Explaining the ill-explained ways to obtain a consensus sequence in BioRuby.

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 …

What works - NGS assemblers

A quick paper review on picking the best assembler

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 …

Drawing sequence logos

A very simple script to do a simple but tedious task.

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 …

Reducing a sequence to SNPs

A script for a simple task.

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 …