Editing Portal:Life Sciences (section)

=== Model organisms and comparative genomics ===

The Human Genome Project did not focus only on humans. Model organisms such as yeast, the nematode worm, the fruit fly, mouse, and others were central to genomics. Comparing genomes helped scientists identify conserved genes, regulatory regions, evolutionary relationships, and disease-relevant biology.

Perl was useful in comparative genomics because comparison requires data integration. A researcher might need to compare gene predictions between species, extract orthologs, parse alignment files, query databases, and produce tables linking genes from one organism to genes in another. Perl’s ability to manipulate identifiers, strings, and nested records made it well suited to this work.

Perl scripts were often used to answer questions such as:

* Does this gene have a homolog in another species?
* Which protein domains appear in this gene family?
* Which genes are conserved between organisms?
* Which regions align between two genomes?
* Which annotations changed between database releases?
* Which predicted genes overlap known transcripts?
* Which sequence records are missing or malformed?

Many of these tasks were not single famous “discoveries” but the daily computational work that made discoveries possible.