Mastering Bioinformatics for Beginners

Biological databases organize data into primary, secondary, and specialized types, with DNA gene bank, DBJ, and PDB as key examples.

Navigate the CBI interface to explore gene databases, filter for noncoding or coding genes and human taxa, and examine records with the primary key, attributes, gene IDs, aliases, and coordinates.

Navigate NCBI database to download gene data, choose formats and sorting criteria, and explore a gene's location on chromosome 11, non-coding RNA status, function, and diseases via the gene viewer.

Explore how to store DNA and protein sequences and structure information using diverse file formats, including sequence formats such as faster format and formats like GTF and DF three.

Explore the general feature format (GFF3), a tab-delimited system for annotating features on sequences, including chromosome, source, type, start, end, score, strand, frame, and attributes, and contrast it with GTF.

Explore how genome assembly reconstructs full genomes from dna sequence reads by finding overlaps, joining sequences, and building scaffolds, using mapping against reference or de novo approaches.

Attach biological information to genome sequences by identifying gene locations and coding regions, including introns and exons, and using BLAST or other tools to distinguish structural from functional annotation.

Explore the ensembl genome browser to search genes and variants, compare data across species, and download results in gff3 format. Navigate gene pages with annotations and use variant effect predictor.

Explore the Ensembl gene page using BRCA2 to view stable IDs, sequences, genomic alignments, and transcript models, including exons, coding sequences, untranslated regions, and annotation colors.

Learn how to search for information in Ensemble for human gene data and access trainings, tutorials, workshops, and exercises through the European Bioinformatician Institute to build practical bioinformatics skills.

Explore how polymerase chain reaction enables DNA amplification, including real time reverse transcription PCR for SARS-CoV-2, primer design, denaturation, primer annealing, and DNA extension in diagnostic applications.

Design PCR primers by optimizing length 18–24 bp, melting temperature 50–60 C, and GC content 40–60%, then assess hairpin or dimer formation in silico.

Design primers virtually with the Primer-BLAST tool to match your PCR template and gene sequence, using accession numbers from NCBI and optimized primer parameters.

Explore sequence alignment to compare biological sequences and reveal functional, structural, or evolutionary relationships, covering pairwise, multiple, global, and local alignments with tools such as Emboss, Needleman-Wunsch, Smith-Waterman, and Blast.

Learn to use BLAST for local alignment, choose the right BLAST form (nucleotide BLAST, protein BLAST, BLASTX), enter sequences, and interpret e-values, identities, and gaps to identify homologous genes.

Explore multiple sequence alignment with MUSCLE to compare five HIV-1 env protein sequences, retrieving data from Uniprot and visualizing conservation and evolutionary relationships.

Celebrate completion of the bioinformatics course, thank students for their hard work, invite feedback on this course and future ones, and wish them a bright, accomplished future.