Appunti VERIFICATO
Programmazione per bioinformatica
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- DNA File Formats and Processing:
- Explores ASN, FASTA, and Genbank formats; Genbank offers richer metadata.
- Details DNA string compression (bits to hex) and provides Python functions (
DecoderDict,DNAFromASN1) for decoding.
- Principal Component Analysis (PCA):
- Utilized for dimensionality reduction in high-dimensional biological data.
- Protocol involves computing covariance, eigenvectors/eigenvalues, and projecting data to simplify analysis.
- Effectively used for comparing genomes, classifying bacterial types based on codon frequencies, as illustrated by visual clustering.
- Genetic Sequence Analysis:
- Discusses codon frequencies as a basis for classifying genomes, with a Python function (
CountCodons) to count them. - Highlights the complexity of sequence alignment due to indels (insertions/deletions) and varying sequence lengths, precluding brute-force methods.
- Mentions the BLOSUM50 matrix, a standard for protein sequence alignment, considering amino acid substitution probabilities.
- Discusses codon frequencies as a basis for classifying genomes, with a Python function (
- Information Theory and Protein Biology:
- Introduces Shannon's Entropy of Information, a measure of data unpredictability and complexity, vital for understanding data encoding.
- Outlines challenges in protein production, such as inclusion body formation, influenced by factors like temperature, concentration, redox environment, and molecular interactions.
- Advanced Sequencing Technologies:
- RNA-Seq: An unbiased method for transcriptomic analysis (isoforms, SNPs, fusions), offering superior dynamic range and de novo capabilities compared to microarrays.
- ChIP-Seq: Leverages Next-Generation Sequencing (NGS) to map protein-DNA interactions across the genome.
- Whole-Genome Bisulfite Sequencing (WGBS): A key epigenetic tool for comprehensive analysis of DNA methylation patterns, linked to disease.
- Comprehensive Glossary:
- Defines numerous essential bioinformatics terms, including
Coverage level,CpG site,Deep sequencing,Epigenetics,GWAS,NGS,SNPs,Targeted resequencing,Transcriptome, andWGS. - Includes a list of key acronyms relevant to the field.
- Defines numerous essential bioinformatics terms, including