Introduction to Genome Annotation, 1 hp

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

Application form

Important dates

Application open: December 16

Application deadline: March 15

Confirmation to accepted students: March 22

Responsible teachers: Henrik Lantz

If you don’t receive information according to the dates above, contact

Course fee

A course fee of 1000 SEK will be invoiced to accepted participants (includes the study material, coffee, lunches and course dinner). NOTE – Uppsala University cannot invoice individuals.

Course content

Course webpage

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
·       The NBIS annotation service

Entry requirements

Participants must be comfortable navigating a linux shell and execute 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 (genome assembly, transcriptome assembly, SNP calling) is a plus. Applicants are also encouraged to bring their own laptops, but there will be computers to use for participants unable to do so.

Due to space constraints for the computer exercises, there are a maximum number of allowed 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.