Sequence Alignment Algorithms — Pairwise & Multiple

Gain expertise in pairwise and multiple sequence alignment, scoring theory, and automated reporting with reproducible, real-world practical sessions.

Sequence Alignment Algorithms (Pairwise/Multi)

Session Index

Session 1

Fee: Rs 6300

Pairwise Alignment Foundations

Global vs local alignment: Needleman–Wunsch & Smith–Waterman

Theory

Gap models: linear, affine, convex penalties & traceback logic

Affine gaps Traceback Dynamic programming

Sensitivity vs speed trade-offs & accuracy diagnostics

Score distributions E-values ROC/AUC

Session 2

Fee: Rs 8400

Scoring, Matrices & Heuristics

Substitution matrices: PAM/BLOSUM choice & calibration

PAM BLOSUM Dayhoff

Heuristic search & database alignment at scale

BLAST+ DIAMOND MMseqs2

Statistics, filtering & multiple-hypothesis handling

E-value FDR/q Coverage%

Session 3

Fee: Rs 11200

Multiple Alignment & Trimming

MSA strategies: progressive, iterative, HMM profile methods

Clustal Omega MUSCLE MAFFT

Guide trees, alignment trimming & consensus building

FastTree trimAl EMBOSS cons

Visualization & quality metrics for MSA outputs

AliView Jalview pp-score

Session 4

Fee: Rs 14000

Mini Capstone: Alignment Pipeline

Design end-to-end alignment workflow & evaluation plan

Theory

Automate pairwise/MSA with reporting & visualization

Snakemake Python MultiQC

Benchmark on curated datasets & prepare publication-ready figures

pandas matplotlib JupyterLab

PDF

Sequence Alignment Algorithms (Pairwise & Multiple) Training | NW, SW, MSA, BLOSUM/PAM