Sequence alignment, BLAST, HMMs, genome assembly, variant calling, RNA-seq, ChIP-seq, proteomics.
Omics And Bioinformatics
Sequence alignment
Arrangement of biological sequences (DNA, RNA, protein) to identify homologous residues. Global (Needleman-Wunsch 1970) or local…
BLAST (Basic Local Alignment Search Tool)
Altschul-Gish-Miller-Myers-Lipman 1990 heuristic sequence-similarity search. Seeds high-scoring words, extends ungapped, reports…
Hidden Markov model (bio applications)
Probabilistic model with hidden states emitting observations. Profile HMMs (HMMER) for family membership; gene prediction (GeneMark,…
Genome assembly
Reconstruction of a genome from sequencing reads. De novo (no reference) via OLC or de Bruijn graph; reference-based (mapping). Challenges:…
Variant calling
Detection of SNVs, indels, structural variants from aligned reads. Bayesian genotype likelihoods (GATK, DeepVariant). Filters: allele…
RNA-seq
Transcriptome sequencing: fragment cDNA → sequence → align → count. Differential expression by DESeq2, edgeR (negative binomial).…
ChIP-seq
Genome-wide protein-DNA-binding assay: crosslink → ChIP with antibody → sequence → align → peak call (MACS). Maps TF binding sites, histone…
Single-cell RNA-seq (scRNA-seq)
Transcriptome profiling at single-cell resolution via droplet (10x Chromium) or plate (Smart-seq2) methods. Analysis: doublet detection,…
Multiple sequence alignment
Progressive alignment (ClustalW), consistency-based (T-Coffee, MAFFT), profile methods. Foundation for phylogenetic inference, motif…
Functional annotation (GO, KEGG)
Gene Ontology: structured vocabulary of biological process, molecular function, cellular component. KEGG pathways. Enrichment analysis…