Practical Bioinformatics
Lecture 6
Translation & Intro to Sequence Alignment
Classroom Code: izgfajp
Summary and Recap of Strand Information
Leading and Lagging Strands: DNA Replication
Remember: DNA Polymerase can only add bases in the 5’ to 3’ direction, hence
reads in the 3’ to 5’ direction
Coding and Non-coding strands: RNA Transcription. For the same reason
above, RNA polymerase reads the non-coding strand to produce a sequence
identical to the coding strand (except that it contains U). Thus the Template strand
is the non-coding strand!
+/- strand
Importance
In bioinformatics, annotating genes or predicting coding regions requires
understanding which strand is the coding strand (sense) and which is the template
strand (antisense).
Example: In bacterial genomes, genes are often densely packed on both strands,
so it’s crucial to distinguish coding from non-coding strands. Misinterpreting the
strand can lead to incorrect predictions of mRNA or protein sequences.
Practical Importance:
FASTA files store sequences as one strand (typically 5' to 3'). For gene annotation,
bioinformaticians must determine whether the stored strand represents the coding
strand or the template strand for each gene.
Importance for Next Generation Sequencing
Strand Bias in Sequencing: DNA sequencing methods can introduce strand bias
during library preparation. Bioinformaticians filter out extreme strand bias.
Tools for variant calling (e.g., GATK, bcftools) identify SNPs, indels, and structural
variants in genomic data. Tools like ANNOVAR, VEP, and snpeff predict variant
effects (e.g., missense, nonsense, or silent mutations) based on strand-aware
annotations.
RNA polymerase transcribes the template strand, producing an RNA transcript
matching the coding strand. Bioinformatics tools like HISAT2, STAR, and kallisto
align RNA reads to the genome and infer expression levels. Misidentifying strands
can result in errors in understanding gene expression.
What are Variations?
- Mutation: change of one nucleotide to another that changes function
drastically (frequency < 1% in the population)
- Single Nucleotide Polymorphisms (SNPs): change of one nucleotide to
another with frequency > 1%. E.g. Codon 72 of TP53 can be CGC (Arginine)
or CCC (Proline), representing a common SNP in the population. This
variation has been studied for its potential association with cancer risk.
- Insertion/Deletion Polymorphisms (INDELs) - small mutations removing or
adding one or more nucleotides at a particular locus. E.g. BRCA1 gene
mutation: Normal DNA: ...GATCCAGCTAG… ; Mutated DNA (deletion):
...GATC---CTAG...
- Structural Variation (SVs) - medium to large sized rearrangements of
chromosomal DNA
DNA Level
(Code)
RNA Level (Codons)
Amino Acid Classes
Translation: Closing the Central Dogma of Life
Translation
Translation
