One of my recent projects has been to map short sequences of DNA (tags) to specific positions in transcripts (ie. exons, introns, UTRs). Everything was going along nicely, until I was looking through my output data and saw something weird.

I had one sequence map itself to an exon and a 5′UTR - on the same transcript. This caused me some concern (and an afternoon of frustration), because it seemed that according to the Ensembl database, this one position is both an exon and a 5′UTR. I thought I had done something wrong in my code, such as calculating the start and end position of the UTRs wrong or pulling out the wrong starting position for the start of translation.

Seems that wasn’t the problem. What it turned out to be was partially my fault, but also partially the fault of the Ensembl gene annotation.

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Posted: July 15th, 2007 under bioinformatics, hmmmmm.
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I recently stumbled upon this paper:
Conversion of amino-acid sequence in proteins to classical music: search for auditory patterns
Rie Takahashi & Jeffrey H Miller
Genome Biology 2007, *8*:405

_”The primary goal of this work is to convert genome-encoded protein sequences into musical notes in order to hear auditory protein patterns.”_

This is an interesting - and unique - approach to analyzing protein sequences. They’ve taken many things into consideration, including codon distribution and amino acid frequency. They’ve developped rules for rhythm, range, dynamics and note lengths. Unlike previous efforts which have tried to directly translate an amino acid to a musical note, this approach uses chords and musical rules to generate these compositions.

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Posted: July 8th, 2007 under bioinformatics, unique.
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