from Hacker News

Investigating a new respiratory virus outbreak in Santa's workshop

by oalders on 12/20/24, 10:57 PM with 2 comments

• by mdperry on 12/21/24, 11:14 PM

  I was toying with posting this here as "One-Quarter of my Life with Perl" (riffing on Randal's talk title) (16 yrs x 4 was close enough for government work), but I refrained. After surveying popular social media sites (i.e., reactions to this Perl Advent Calendar entry), I now appreciate that some folks may be triggered by the subject matter. Our friend and fellow Perl-er, Lincoln Stein, wrote an article for The Perl Journal (TPJ) back in the day, called "How Perl Saved the Human Genome Project" https://bioperl.org/articles/How_Perl_saved_human_genome.htm...

• by Terr_ on 12/20/24, 11:24 PM

  Using Perl for sequence alignment? Oof, I did not expect to be blindsided with such an incredibly esoteric flashback to one bioinformatics class many years ago.

  I eventually ended up rewriting the thing into an excessive Java/Swing program which animated its work through all the comparisons, showing show best paths and dead-ends. It involved a BLOSUM64 matrix, so I must've been aligning based on what amino acids were being coded-for, even if underlying base pairs differed.