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🧬 Bioinformatics & Computational Biology

Sequence Analysis • Genomics • Proteomics • Phylogenetics

Explore 45+ bioinformatics algorithms and tools — from sequence alignment and genome assembly to protein structure prediction and evolutionary modeling.

48+

Bioinformatics Methods & Biological Data Science

Needleman-Wunsch

Global alignment, dynamic programming, affine gap penalties.

Smith-Waterman

Local sequence alignment, maximum similarity substrings.

BLAST

Basic Local Alignment Search Tool, heuristic, word seeds.

Multiple Sequence Alignment

ClustalW, MUSCLE, progressive alignment, MAFFT.

Genome Assembly

Overlap-layout-consensus, de Bruijn graphs, SPAdes.

Variant Calling

SNPs, indels, GATK, FreeBayes, SAMtools.

RNA-Seq Analysis

Transcript quantification, differential expression, DESeq2.

Transcriptomics

ChIP-Seq / Epigenomics

Peak calling, histone modifications, DNA-protein binding.

Phylogenetic Trees

UPGMA, Neighbor-Joining, maximum parsimony, bootstrapping.

Maximum Likelihood & Bayesian

RAxML, MrBayes, substitution models (GTR).

Protein Structure Prediction

Homology modeling, ab initio, AlphaFold, Rosetta.

Molecular Docking

AutoDock, ligand-receptor interactions, scoring functions.

Protein Data Bank & Visualization

PDB format, PyMOL, Chimera, structure validation.

Motif Discovery (MEME)

Position weight matrices, consensus sequences, transcription factors.

Hidden Markov Models (HMM)

Profile HMMs, gene finding, Pfam, domain detection.

Next-Generation Sequencing (NGS)

Illumina, PacBio, Oxford Nanopore, read quality (FASTQ).

Read Alignment (BWA, Bowtie)

Burrows-Wheeler transform, SAM/BAM files.

Synteny & Comparative Genomics

Genome rearrangements, orthologs, MCScanX.

CRISPR-Cas9 Guide Design

Off-target prediction, sgRNA efficiency scoring.

Biological Databases

GenBank, UniProt, Ensembl, NCBI, PDB, RefSeq.

Gene Ontology (GO)

Biological process, cellular component, molecular function.

KEGG & Pathway Analysis

Metabolic pathways, signaling, pathway enrichment.

Systems Biology

Suffix Trees & Genome Indexing

FM-index, Burrows-Wheeler, pattern matching in DNA.

String Algorithms

de Bruijn Graphs

k-mers, Eulerian paths, genome assembly (Velvet, SPAdes).

GWAS & Population Genetics

LD, Manhattan plots, polygenic risk scores, PLINK.

Metagenomics & Binning

16S rRNA, shotgun, MAGs, kraken, metaSPAdes.

Single-Cell RNA-Seq

Dimensionality reduction, clustering, Seurat, scanpy.

Transcriptomics

🧬 Bioinformatics Learning Pathway

🧪 Foundation

Sequence alignment (global/local), biological databases, FASTA/GenBank.

🔬 Analyst

BLAST, phylogenetics, RNA-Seq, variant calling, GO analysis.

⚙️ Computational Biologist

Genome assembly, HMMs, protein structure, de Bruijn graphs, CRISPR design.

🧬 Research Leader

GWAS, single-cell omics, metagenomics, AlphaFold, evolutionary modeling.

🧪 Decode Life with Data Science

Access interactive notebooks, real genomic datasets, and bioinformatics pipelines.

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