National course open for PhD students, postdocs, researchers and other employees in need of Genome Annotation skills within all Swedish universities

Important dates

• Application open: February 6
• Application deadline: April 8
• Confirmation to accepted students:  one week after application closes

Responsible teacher/s: Henrik Lantz

Contact information for questions regarding the course: Henrik.lantz@nbis.se

Course fee

A course fee of 1700 SEK will be invoiced to accepted participants (includes the study material, coffee, lunches and a course dinner).

Course content

National course open for PhD students, postdocs, researchers and other employees in need of Genome Annotation skills within all Swedish universities

Genome annotation is the process in which loci of interest in a genome are identified, both in structure and function. The structural part includes identifying the number and size of exons and introns, size of UTRs, and number of isoforms. The functional annotation, in turn, focuses on inferring the biological role of different transcripts.

The course is aimed at researchers that are involved in on-going or upcoming genome projects and wish to deepen their understanding of the various forms of data and computational steps required to achieve a comprehensive annotation. The focus of the course will be on non-model eukaryote organisms, and in particular the structural annotation of protein coding genes. We will use de novo gene finders, protein alignments and RNA-seq data to infer the structure of genes, and show how to combine these different lines of evidence to get the most stable and informative annotation. We will also infer the function of these genes using similarity to known proteins as well as the presence of functional domains.

Topics covered will include:

• Project planning
• Gene finders
• Protein alignment
• RNA-seq assembly
• Combined structural annotation using Maker2
• Functional annotation
• Prokaryote annotation

Entry requirements

Participants must be comfortable navigating a linux shell and executing programs from the command line. Without this knowledge, it will be impossible to participate in the computer exercises. Previous experience from working with NGS data is beneficial. Applicants are encouraged to bring their own laptops, but there will be computers to use for participants unable to do so.

Due to limited space the course can accommodate a maximum of 18 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.

Registration form 

Registration closed