Bioinformatics Checking Characters in Nucleotide Strings The other day I was solving the wrong problem. Before hashing, mash has to verify that all characters in a k-mer come from one specific alphabet (either nucleotide, ACGT; or protein). I tried
Bioinformatics PFASTA — Yet another set of FASTA tools Recently more and more CVEs are being filed against bioinformatic tools. Validity of the bug reports aside, it just shows that the security aspects of scientific software becomes more interesting. One of the
Bioinformatics Optimizing Mash Mash could well be the new BLAST. It is a great technique to compute similarity scores for sequences. However, its implementation is not optimal. In this blog post I describe some tricks to
Bioinformatics Static Libraries Parsing a FASTA file or any file format can be hard. But mostly writing a parser can be cumbersome. Thus, people don't do it properly or just copy someone elses work. For reading
Introducing AlnMassage Each good scientific experiment should start with an hypothesis. This is true also for sequencing in the age of NGS. However, often enough the data doesn’t fit the expectations. In this case
Bioinformatics strlen(genome) Genomes are very long strings. This comes to no surprise to anybody, except maybe a few C programmers. The following bug appears only in C programs or bad C++ programs due to the
Bioinformatics FASTA “A QA Engineer walks into a bar. Orders a beer. Orders 0 beers. Orders 999999999 beers. Orders a lizard. Orders -1 beers. Orders a sfdeljknesv.” FASTA is the simplest file format ever invented
Bioinformatics RSPR RSPR is a tool to compute a topological distance between two phylogenies. It is an alternative to the Robinson-Foulds distance. The canonical implementation rspr has supports many different algorithms and options. Unfortunately, the
Bioinformatics INDELible INDELible is one of the most sophisticated simulators for sequence evolution. It supports plenty of different sequence evolution models, various indel distributions, basically everything you could wish for. As such the code is
Bioinformatics MUMmer MUMmer is one of the most used sequence alignment tools, right after BLAST. Most of its code base is quite old but still being actively developed (see MUMmer4). The following issue has been
Bioinformatics The State of Software Engineering in Bioinformatics This post will kick off a series of blog posts about the state of software engineering in bioinformatics. In each post I will take a stab at a popular tool in bioinformatics, dive
Errors in the Ensembl Genomes Database The Ensembl Bacteria database contains more than 2600 whole genomes sequences of Escherichia coli. It should not be a surprise that some of this data will be flawed. As a simple verification I
Avoid mutable by-value-capture in C++ Here is a quirks I stumbled upon in modern C++. As an example we will be printing all odd numbers in a vector and the count of odd number so far. For the
How to write a zsh completion zsh, an alternative to bash, is known for its superior completion system. This provides the user with a convenient way to input arguments and options to a command. It really is a time
Learning Perl in 2017 For a course on genetic analysis I was required to learn Perl (5). I now spend a week with two books and must say that not only did all my prejudices against Perl
Spielbericht E2 Die Einsiedlerin Die Einsiedlerin ist das zweite Abenteuer aus der Spielsteinkampagne für Das schwarze Auge. Nach etwa zweieinhalb Sitzung haben meine Spieler gestern das Tal wieder verlassen. Anbei ein Bericht, was mir an dem Abenteuer
The Missing Cow Call Linux allows users to allocate memory via mmap(2). This can then be shrunk, grown, and moved by mremap(2). The feature of the last syscall is that no data actually gets copied.
Bezahlter Inhalt Die Tage erreichte mich per Mail die folgende Anfrage (persönliche Daten redigiert). Hallo Fabian Kloetzl, für meine Kunden suche ich hochwertige Artikelplätze mit thematischem Bezug. Ein konkretes Interesse meines Kunden auf Ihrer Seite
A Compiler Bug Today, I was trying to validate some user input with C++11's new regular expressions. In essence, I tried the following. auto r = std::regex("[0\\- ]"); std::cout <<
dsa Tumult in Oberbüll Erst neulich ging das Scriptorium Aventuris online. Es erlaubt dem kreativen DSA-Fan seine eigenen Werke zum Download zur Verfügung zu stellen. Letzteres sogar gegen ein Entgelt. In diesem Post möchte ich mein Kurzabenteuer
dsa Fuzzy Logic im Rollenspiel Dies ist ein Post im Rahmen des Karnevals der Rollenspielblogs vom Oktober 2016 mit dem Thema Quellcode, Binärcode und Fuzzylogic. Was haben drei Begriffe aus der Informatik mit Rollenspiel zu tun? Eine ganze
z-push bei uberspace So richtig funktioniert das alles nicht. Hat jemand eine Idee, was ichvergessen habe? Mich störte schon länger, dass Mails auf meinem Desktop ankamen, bevor sie auf mein Telefon gepusht wurden. Dies konnte ich
Epson PULSENSE 20-0101-0008 To save battery life I disconnected my Epson PULSENSE watch from my phone for a few days. When I tried to reconnect, I always got the error 20-0101-0008. But finally I managed to
On Bootstrapping Whole Genomes Bootstrapping has been the de-facto standard for computing support-values of phylogenies for decades; and it has served us well. However, with the rise of high-throughput sequencing its limits became apparent. Not only is
The Fastest Way to Compute the Reverse Complement Bit-twiddling on genomes seems to become a regular pattern in this blog; See calculating the gc-content and hashing nucleotides. Today I will go into details on computing the reverse complement. Complementing Ever since
