genome annotation

genome annotation

the process of converting a raw DNA sequence of a genome into a meaningful biological interpretation- identifying genes, transcripts, and regulatory regions using bioinformatics tools

alternative splicing

allows one gene to produce multiple mRNA transcripts by joining exons in different combinations, leading to different protein isoforms in various tissues or conditions

pseudogenes

relics of ancient genes that accumulates mutations - non-functional DNA sequences that resemble real genes but have lost their ability to code for protein

What is a typical structure of a eukaryotic gene?

Promoter → Exons (coding regions) → Introns (non-coding regions) → UTRs (untranslated regions).

How do eukaryotic and prokaryotic genes differ?

• Eukaryotes: Genes contain introns and exons, mRNA is processed (splicing, capping, polyadenylation).

• Prokaryotes: Genes are continuous (no introns), often organized in operons, and transcription and translation occur simultaneously.

What is a “long ORF”?

A long Open Reading Frame — a stretch of DNA without stop codons that could encode a protein.

codon usage bias

coding sequences use certain synonymous codons more frequently; these patterns can help identify likely coding regions.

ribosome binding site (RBS)

A sequence (e.g., Shine–Dalgarno: AGGAGG) in prokaryotes ~8 bp upstream of the start codon that helps recruit ribosomes for translation initiation.

common promoter sequences in eukaryotes and prokaryotes

• Eukaryotes: TATA box (~25 bp upstream), CAAT box.

• Prokaryotes: -10 (Pribnow box) and -35 elements.

start and stop codons typically used in gene prediction

• Start codons: ATG (common), sometimes GTG or TTG in prokaryotes.

• Stop codons: TAA, TAG, TGA.

What are examples of small non-coding RNAs and their functions?

• miRNA: Post-transcriptional gene silencing

• siRNA: mRNA degradation

• piRNA: Genome defense (especially against transposons)

promoters

DNA sequences near transcription start sites that bind RNA polymerase and transcription factors to initiate transcription.

epigenetic marks

Chemical modifications such as DNA methylation and histone modification that affect gene expression without changing DNA sequence