Editing Portal:Life Sciences (section)

=== Relationship to past discoveries ===

Perl’s contribution to past biological discoveries was usually indirect but essential. Perl helped scientists make sense of the raw material of genomics: strings, files, identifiers, coordinates, annotations, database records, and logs.

A gene discovery, disease association, genome annotation, or comparative-genomics result might appear in a paper as a biological conclusion. Behind that conclusion, however, there were often scripts that cleaned input data, matched identifiers, ran searches, parsed results, and produced evidence tables. In the 1990s and early 2000s, many of those scripts were written in Perl.

Perl helped make possible the routine computational work behind:

* early genome assemblies;
* annotation of human and model-organism genes;
* comparative analysis between species;
* protein-family classification;
* sequence-similarity searches;
* management of public genome databases;
* processing of high-throughput sequencing data;
* integration of laboratory and computational records.

In this sense, Perl was part of the infrastructure of discovery. It was often invisible in final publications, but it was present in the pipelines, databases, and scripts that allowed the discoveries to happen.