What is base calling and gene calling?

[Sh. Akbar]

What is base calling? and gene calling? are these related?

[Fazil Hussein]

Both base calling and gene calling are essential steps in analyzing genetic data, but they address different aspects.

Base Calling:

Definition: Base calling is the process of translating raw data from a sequencing machine into a sequence of nucleotides (A, C, G, T or U).
Input: Electrical signals, light intensity signals, or chromatogram peaks generated during sequencing.
Output: A string of letters representing the sequence of nucleotides in the DNA or RNA molecule.
Examples of algorithms: Phred, Bonito, PoreCNN
Importance: Base calling is the first step in processing and analyzing genetic data. It is crucial for accurate downstream analyses like variant calling, gene expression studies, and genome assembly.

Gene Calling:

Definition: Gene calling is the process of identifying and annotating genes within a DNA sequence.
Input: A DNA sequence generated after base calling.
Output: Annotations of predicted genes, including their location, start/stop codon, coding region, and potential function.
Examples of algorithms: GeneMark, Augustus, SNAP
Importance: Gene calling helps us understand the functional elements in a genome, predict protein sequences, and identify disease-causing mutations.

Relationship:

Direct: Base calling is a prerequisite for gene calling. To identify genes, we need a reliable sequence of nucleotides as input.
Indirect: Base calling errors can propagate to gene calling errors. Therefore, accurate base calling is crucial for reliable gene predictions.
Complementary: While base calling focuses on individual nucleotides, gene calling looks at larger patterns and identifies functional units within the sequence.

Together, base calling and gene calling form the foundation for various downstream analyses in genomics and contribute significantly to our understanding of genes, genomes, and their functions.

 

Source: Bard.

[BioHub]

Short answer:

Base calling is the process of assigning nucleobases to chromatogram peaks or electrical current changes resulting from the nucleic acid sequencer.

Gene calling is the process of identifying regions of genomic DNA that encode genes.

Variant calling is the identification of differences or variants in a sequenced genomic DNA when compared to a reference genome.

 

Source: Glossary

 

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