Another Bioinformatics Blog

I finally upgraded to Snow Leopard, and I was very happy until I wanted to use ports (the geek heart of Mac).  The first issue: Ports doesn’t work!

Today I had an unusual request for a bioinformatics course: can you give me the raw reads from the 3 longest contigs?  She was talking about an ongoing genome project, and she wanted me to extract the sequences and quality values only for the 454 reads assembled in a given contig (the reads before assemblage, off course).  It sounds like a huge task including a .ace parser, a fasta parser, a fastq parser, and may be an SFF parser.  However, all is already done: viva AMOS!

I had an issue installing the AMOS GUI software for visualizing assemblies because of Qt3, now solved!

A frequent problem: several algorithms for the same task leads to several implementations, and several implementations plus no universal standard leads to a messy collection of output files.  How can I compare those results? build a script.  On this episode: how to compare sequence regions by their coordinates?

Some weeks ago I had an issue with dotur.  I wanted a beautiful rarefaction plot, with 4 curves at 100%, 99%, 95% and 90% of sequences similarity.  However, dotur (the software that generates the rarefaction plot data) acepts the standard dnadist (from phylip) output format, but not the similarity table.

Some days ago a labmate had freak troubles with glim-extract (from Glimmer), and he asked me to write a script for the extraction of a set of predicted genes from a draft genome.  The result:

After the Ubuntu 7.10 upgrade panic of Tuesday, I upgraded to 8.04, and finally to 8.10 this server.  Everything went OK, I was happy: ANY ERROR!  However, two minutes later I tried to open a pdf with evince, and guess what…

evince: symbol lookup error: /usr/lib/libgio-2.0.so.0: undefined symbol: g_thread_gettime

Most of you know about the importance of maintain a server running, specially when the server is the main server!. The story: a server running Ubuntu 7.04, without any troubles, everything good, but one day the guys of archives.ubuntu.com no longer stores the universe packages on their servers, making “apt-get update” crash once and again. Solution 1: don’t use the universe repositories, good on the short time, but not so good for the long time, specially when you need every sort of packages to make the bioinformatics software run. Solution 2: time to upgrade.

La definición de esta disciplina se ha debatido desde sus principios entre la biología molecular, las matemáticas, la estadística y las ciencias de la computación, y más recientemente se ha extendido hacia otras ramas de la biología como la genética y la ecología.  De cualquier modo, como la mayoría de ciencias y disciplinas, la bioinformática se resiste a encajar con precisión en sus definiciones, por lo que no me ocuparé de precisarla, listando en su lugar algunas definiciones previamente propuestas y algunos de los enfoques que le han sido dados.