1: Modules
- Page ID
- 187434
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)- 1.1: BLAST (AKA so you have a sequence)
- This page explains the BLAST (Basic Local Alignment Search Tool) algorithm for analyzing DNA sequences by identifying similar sequences in databases. It covers the mechanics of BLAST, including scoring matches using a similarity matrix and the concept of Maximal Segment Pairs (MSP). Variants of BLAST, such as BLASTn and BLASTp, are introduced for specific sequence comparisons, enhancing understanding of sequence homology.
- 1.2: DNA Sequencing
- This page covers essential DNA sequencing methods in bioinformatics, including Sanger, Illumina, PacBio, and nanopore technologies. It explains the principles, pros, and cons of each method, noting Sanger's high accuracy for small datasets and the scalability of next-generation sequencing (NGS).
- 1.3: Genome Assembly
- This page covers genome assembly, outlining methods to reconstruct DNA sequences using overlap and De Bruijn graphs for better error handling. It emphasizes evaluating assembly quality through contig metrics and BUSCO for validating single-copy genes. The importance of minimizing contig numbers while maximizing length and using k-mer analysis to identify errors in assemblies is also highlighted.
- 1.4: Genome Alignment
- This page covers sequence alignment in bioinformatics, emphasizing the significance of aligning genomic sequences for evolutionary analysis. It explains concepts like matches, mismatches, and gap penalties, and introduces key algorithms such as Needleman-Wunsch for global alignment and Smith-Waterman for local alignment. Multiple Sequence Alignment (MSA) methods, including MAFFT, MUSCLE, and ClustalOmega, are highlighted.
- 1.5: Gene Annotation
- This page covers gene annotation, which includes identifying DNA sequences related to protein-coding genes through structural and functional annotation. It explains start and stop codons, the identification of open reading frames (ORFs) in prokaryotes and eukaryotes, and the role of introns and regulatory sequences. Position-Specific Scoring Matrices (PSSMs) and methods for exon identification are discussed.
- 1.6: Gene Expression Analysis
- This page covers gene expression analysis, detailing mRNA quantity assessment, sequencing processes, and alignment techniques using Bowtie. It highlights normalization challenges and stresses the importance of quality control in RNA-seq, along with methods for handling batch effects. Statistical models are discussed for determining gene expression across tissues, with an emphasis on p-value adjustments, including the Bonferroni correction and Benjamini-Hochberg procedure.
- 1.7: Protein Structure
- This page covers protein structure, highlighting the importance of primary, secondary, tertiary, and quaternary structures for function. It details experimental methods like X-ray crystallography and NMR for determining structures, and introduces the Protein Data Bank as a key resource.