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Introduction to Genome Annotation, 1 hp
| Kursnummer | 50,5 |
| År | 2017 |
| Typ | Methodcourse |
| Spår | - |
| Max antal deltagare | 20 |
| Sista ansökningsdag | 2016-03-30 |
| Språk | En |
| Kursansvarig | Henrik Lantz |
| Institution | SciLifeLab |
| Besöksadress | Uppsala biomedicinska centrum BMC Husarg. 3 751 23 Uppsala |
| Postadress | Administrativt centrum för SciLifeLab i Uppsala Box 3037 750 03 Uppsala, |
| Datum | 2017-05-09 to 2015-05-11 |
| Lokal | E10:1308/1309 (Trippelrummet, Navet) |
| Kurslängd | 3 days |
| Kursrapport | |
| Kursplan |
Beskrivning
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.
Innehåll
Topics covered will include:
· Project planning
· Gene finders
· Protein alignment
· RNA-seq assembly
· Combined structural annotation using Maker2
· Functional annotation
· Procaryote annotation
· The NBIS annotation service
Undervisning
Applicants are only accepted via the course page:
https://www.scilifelab.se/events/geneannvt17/
Course fee: 1300 SEK.
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.
Examination
Participation on all lectures, exercises and discussions.
Litteratur
Will be provided during the course
Lärare
Henrik Lantz
Kontakt
https://www.scilifelab.se/events/geneannvt17/
education@scilifelab.uu.se