S.ANNA
Altro PhD (Life Sciences)
Andrea ZUCCOLO
1
20
Y
What is bioinformatics: a historical perspective from 1953 up to the next-gen sequencing;
Similarity searches: intro, basics, global vs local, dynamic programming, dot-plot, fasta, blast scoring matrix; pattern discovery
Following the journey of a genome: from reads to assembly to annotation to comparative genomics:
o Overall sequencing strategy (de novo vs reference based)
o Technical differences (sequencers, strategies: Hierarchical-BAC based, Whole Genome Shotgun, mixed strategies etc.)
o Genome assemblers: greedy graph, OLC, De Brujin's graph based
o The ÒvalidationÓ and Òquality assessmentÓ of a genome assembly
o Annotation: genes, pseudogenes, promoters, transcription factors, repeats (and Transposable Elements)
o Comparisons: SNPs, rearrangements, epigenomic, RNA seq