BIOINFORMATICS

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20 Terms

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due to the massive increase in genetic data, especially during and after the Human Genome Project (2000).

Why did Bioinformatics come about?

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Bioinformatics

It is a multidisciplinary branch of science that integrates computer science, mathematics, statistics, chemistry, and biology to store, retrieve, analyze, and interpret biological data using computational tools.

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To store biological data in structured databases
To develop tools that aid in data analysis
To exploit tools for deriving meaningful biological insights

What are the primary aims of Bioinformatics?

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By sequencing genes like proteases involved in infection, depositing them in public databases, and enabling global access and analysis to support diagnostics and vaccine development.

How does bioinformatics help in studying Schistosoma japonicum?

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DNA → mRNA (via transcription) → Protein (via translation using ribosomes and codons).

What is the central dogma of molecular biology?

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International Nucleotide Sequence Database Collaboration (INSDC)

A triad collaboration between NCBI GenBank (USA), EMBL-EBI (Europe), and DDBJ (Japan) to share and synchronize nucleotide sequence data.

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GenBank

A comprehensive database of publicly available DNA sequences, contributed by researchers and sequencing centers, ensuring open scientific access.

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Locus
Definition
Accession number
Version
Keywords
Source organism
References
Features
Origjn

What key elements are found in a GenBank entry?

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UniProt

A protein sequence and function database that includes reviewed entries and provides structural and functional data. Maintained by EBI, SIB, and PIR.

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Protein Data Bank (PDB)

A repository for 3D structural data of proteins and nucleic acids, primarily from X-ray crystallography, NMR, and cryo-EM studies.

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Immune Epitope Database (IEDB)

A resource cataloging antibody and T-cell epitopes relevant to diseases, vaccine development, allergies, and autoimmunity. Funded by NIAID.

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KEGG

To understand cellular functions and pathways using molecular data from genomics and high-throughput experiments.

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GISAID

A platform for sharing flu and SARS-CoV-2 data, including genetic, epidemiological, and geographic information—crucial for tracking mutations and responses.

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sequence alignment

A method to compare DNA/protein sequences to find similarities.

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Pairwise: Two sequences
Multiple: Three or more sequences
Uses bars (|), dots (.), and colons (:) for degree of similarity

What are the types of sequence alignment

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BLAST

compares nucleotide or protein sequences with databases to find statistically significant matches. Higher Max Score and lower E value indicate better matches.

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Primer-BLAST

A tool for designing PCR primers using Primer3 and checking specificity via BLAST. Ensures primers match the intended template and are unique

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phylogenetic analysis

To reconstruct evolutionary relationships using aligned sequence data, often based on 16S rRNA, producing trees that reflect common ancestry.

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Use BLAST to identify and download related sequences.
Align sequences in MEGA.
Find best DNA model (lowest BIC/AIC)
Construct Maximum Likelihood tree
Adjust tree layout and save

What are the key steps in generating a phylogenetic tree using MEGA?

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Molecular Evolutionary Genetics Analysis MEGA

a free tool for sequence alignment and phylogenetic tree construction.