Complements of Bioinformatics

Provided by: 

S.ANNA

From: 

Altro PhD (Life Sciences)

Lecturers: 

Andrea ZUCCOLO

Semester: 

1

Hours: 

20

Exam: 

Y

Programme: 

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
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