“Working with Zebrafish Genome Resources” Workshop during the 8th European Zebrafish Meeting

This was my first time in lovely Barcelona. I travelled from London the day before the zebrafish meeting kicked-off (in order to be well rested and alert for all the talks and posters!). I attended the “Working with Zebrafish Genome Resources” workshop and I have to say it was absolutely helpful for any scientist working with fish (although the same principles taught can be easily applied to other model organisms). The workshop was organized by the Wellcome Trust Sanger Institute crew, which are experts in the field and provide most of the genomics resourced we use everyday in our work.

It started at 10.30 on the first day of the meeting. The workshop was composed of several modules designed to get an overview of each topic with examples explained by the trainers (which we could follow in our own computers) and with proper discussion of theory and methods. After a general introduction, we started with the hands-on learning.

Even if I knew some things about the topics, I was amazed by such an amount of options for analyzing sequences and how useful it is to handle the available genomic tools in a proper way. The first talks were about manual genome annotation and de novo analysis of sequences, covering some basic resources to access sequence information using Entrez and UniProt, Vega browser and some tools for alignment and open reading frame finders; it was all complemented with hands-on worked examples. Even if some of us were familiar with these resources, it was very helpful to understand the theory behind.

The second part was a deep swimming into genome browsing, using Ensembl, NCBI map viewer and UCSC genome browser. We got a nice idea about why it can be useful to look at the whole genome, and we were demonstrated some of the features and applications of this potent tools. It included more worked examples, which nicely complemented the theory about search and retrieve across the whole genome, basic comparative analysis, features around specific genes and chromosomal regions. Overall it was quite useful.

The third module was to learn how to explore gene function and disease, and sequence variation. A useful search for polymorphisms and their consequences on transcripts and proteins was presented, and how biological pathways associated with those gene products can be altered in several conditions. Even if this module was focused on zebrafish data when possible, disease database were primarily concerned with humans, as there is more sequence variation information for our specie than for zebrafish. However this results in a fantastic way to reinforce the importance of favourite model organism for human disease.

The final module was based on deep comparative sequence analysis. We were shown how to retrieve sequences from different organisms to identify putative homologous genes and compare genomic contexts for potential regulatory function. This is a powerful tool when we want to model human diseases and also for generating transgenic animals. The instructors were very helpful when we got our own genomic problematic sequences and were happy to help us analyzing them.

After this module finished, it was time to register in the zebrafish meeting and the garden party was about to start. The enormous effort of the speakers for organizing this workshop (and patience for helping us one by one!), together with the meeting organizers, made possible a successful experience that will have a good impact in the scientific career of those who attended. The instructors said the workshop would be organized again during the zebrafish meeting in Madison on next year and I really recommend registering on it. Thumbs up for the workshop!

This post is part of a series of posts on the 8th european zebrafish meeting.

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