. 2023 Feb 13;19(2):e1010846. doi: 10.1371/journal.pcbi.1010846

Table 4. Recommended contents for bioinformatics courses embedded in a study path belonging to a BSc degree in computer science-engineering scientific area.

1) Introduction to bioinformatics: rationale, growing importance of data in biology and medicine, the bioinformatics profession (2 hours)

2) Basic elements of molecular biology and genomics (2 hours)

3) DNA sequencing, NGS, reads (4 hours):
    (a) Nucleic acid sequencing platforms: the 3 generations
    (b) From “physical” to “symbolic” data: software for “base calling”
    (c) Coverage, quality of reads, FASTQ, and FASTA formats
    (d) From reads to sequence: assembly algorithms

4) Genomic and proteomic databases: structure and use (8 hours):
    (a) GenBank
    (b) UniprotKB (Swiss-Prot, TrEMBL)
    (c) Exercises: accessing and cross-searching sequences and data

5) Basics of language programming (e.g., R/Python/Julia (1 of choice) (8 hours)

6) Sequence alignment algorithms (8 hours)
    (a) Alignment (local, global, multiple): definitions; optimal alignment, alignment scores, Substitution Matrices
    (b) Alignment algorithms: dynamic programming, heuristic algorithms (BLAST, FASTA)
    (c) Exercises: similarity searches in databases, pairwise, and multiple alignment

7) Algorithms for 2D and 3D structure prediction of proteins (8 hours):
(a) Secondary structure prediction: Statistical-probabilistic methods (Chou and Fasman, GOR)
(b) Tertiary structure prediction: Template-based and template-free approaches

8) Generation and analysis of key homology data and development of pipelines for bioinformatics (8 hours):
    (a) Genomics, proteomics, interactomics data
    (b) Hints at NGS, Microarray, Mass Spectrometry technologies
    (c) Hints at data analysis methodologies: Case-control experiments, Classification, Clustering
    (d) Main packages and workflows for bioinformatics (e.g., Bioconductor, Galaxy, Bio-Linux, Bio-Python)

Course organization (6 CFUs–no less than 48 hours, with possibly 2 ECTS dedicated to classroom exercises). In bold are the contents considered as essential; the non-essential content may be replaced by custom content selected by the teacher.