Unit:
Κατεύθυνση Βιοπληροφορική-Υπολογιστική ΒιολογίαLibrary of the School of Science
Supervisors info:
Βασιλική Οικονομίδου, Αναπληρώτρια Καθηγήτρια, Τμήμα Βιολογίας, ΕΚΠΑ
Ιωάννης Τρουγκάκος, Καθηγητής, Τμήμα Βιολογίας, ΕΚΠΑ
Ιωάννης Μιχαλόπουλος, Ειδικός Λειτουργικός Επιστήμων Β’,Κέντρο Βιολογίας Συστημάτων, ΙΙΒΕΑΑ
Original Title:
Λειτουργικός γονιδιωματικός σχολιασμός σε ευκαρυωτικούς οργανισμούς
Translated title:
Functional Genomic Annotation in Eukaryotes
Summary:
The automatic annotation of genes in a new genome involves finding the boundaries of the genes, their exons, their coding sequences, as well as the discovery of their orthologs in other model organisms. The aim of this work is to compare existing functional genome annotation tools with the ultimate goal of finding the best workflow that will combine a vertebrate genome with protein and nucleotide sequences, as well as transcriptional data and will incorporate the results of ab initio gene finding programs to discover gene boundaries and functionally characterize the genes.
Initially, a target genome will be obtained from the NCBI Genome gene sequence database. The experimental pathway to be followed will be similar to that of the genome annotation of garlic (Allium sativum). Protein-coding genes will be annotated by combining programs at various levels. At the first level, programs for ab initio gene finding, such as GlimmerHMM and sequence homology programs derived from close relatives of the species will be used. The next step is to leverage the available RNA-seq data of the organism and map them against the target genome using programs such as EVM. The final step is the integration of the above results in order to annotate the genes with the highest possible accuracy, generating a GFF3 file.
Main subject category:
Science
Keywords:
Genome Annotation
File:
File access is restricted until 2025-04-08.
Thesis_kaponis.pdf
2 MB
File access is restricted until 2025-04-08.
