Cedric Chauve – guest lecturer (Internationales Gastdozentenprogramm)
Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
… can be found in this github repository.
|First block (16.–27.09.2019)|
|Mon||16.09.||10-12h||Overview: The genomes of 16 Anopheles mosquitoes|
|Wed||18.09.||10-12h||The gambiae phylogeny|
|Thu||19.09.||10-12h||Use synteny for gene family analysis|
|Tue||24.09.||10-12h||Gene-tree species-tree reconciliation|
|Wed||25.09.||10-12h||Fabian: Synteny blocks|
|Thu||26.09.||10-12h||Jan: Improving Scaffolding|
|Andreas: OrthoDB (BUSCO)|
|Second block (10.–14.02.2020)|
|Mon||10.02.||10-12h||The genome rearrangement landscape|
|Tue||11.02.||10-12h||Handling duplications / Small parsimony problem (SPP)|
|Wed||12.02.||10-12h||Ancestral gene orders in a model-free framework|
|Thu||13.02.||10-12h||Joint scaffolding and ancestral gene order reconstruction|
This seminar is composed of two blocks and can ideally be combined with the lecture "Algorithms in Comparative Genomics" that is part of the same module (Special Algorithms in Bioinformatics).
In a first block, methodological gaps will be closed between basic aspects covered in the module “Sequence Analysis” and topics of the above mentioned lecture “Algorithms in Comparative Genomics” that will take place after this seminar block during WS 19/20. In the second block after the lecture, advanced, applied topics will be discussed.
With the increase in the number of available genomes sequenced with the Illumina technology, comparative genomics projects consider large groups of species, whose genomes are often provided in the form of very fragmented assemblies. This creates challenges to apply classical comparative genomics algorithms, especially for the analysis of genome rearrangements that often assume the considered genomes are provided fully assembled. A typical recent example of this is provided by a recently sequenced group of 21 genomes of mosquitoes of the genus Anopheles that include the major malaria vectors. In this group of genomes, of primary importance from a public health point of view in many tropical countries, understanding the evolution of gene order is crucial especially toward associating gene order genotypes to ecological phenotypes, such as the resistance of insecticides. The purpose of the proposed course is to illustrate the various challenges posed by such data within comparative genomics projects and to introduce protocols, algorithms and tools that address these challenges, using the Anopheles dataset. We will provide first-hand experience on the analysis of these motivating data (Science, 2015; BMC Genomics, 2018).
In the detailed descriptions below, topics correspond to one scientific article each that is to be prepared, presented (30-45 minutes talk) and summarized (5-10 pages) by a student as required by the module requirements, and discussed by the group. Further individual topics are available if required.
In addition to the above standard procedure, we will provide computational results on actual experimental data, which the students can analyze and use to enrich both the content of their presentation as well as their experience with working on real data.
In the first block of the seminar (in preparation of the lecture), we will consider the problem of generating, from the provided genome assemblies and sequence data, the gene orders necessary in order to study the evolution of the gene order of the considered genomes. This will cover the following aspects:
At the end of this block, students will have worked through the major steps required to process input genomes toward the analysis of genome rearrangements as required by the models and methods that are taught in the subsequent, complementary lecture.
The second block will address advanced applied topics, especially towards the fact that the provided genomes contain relatively few single-copy orthologs and are highly fragmented. We will study the following aspects.