Re: Lisp Driven Genomics in Nucleic Acids Research

Damn! A top billing for Lisp (even tho "This algorithm is the central contribution of this work.") calls for a top post!

:)

kt

JShrager@xxxxxxxxx wrote:
Our paper:

M Jain, J Shrager, E Harris, R Holbrook, A Grossman, and O Vallon
(2007)
EST assembly supported by a draft genome sequence: an analysis of
the
Chlamydomonas reinhardtii transcriptome.

has just appeared in the journal Nucleic Acids Research (NAR).

The paper is freely available here:

http://nar.oxfordjournals.org/cgi/content/full/gkm081v1?ijkey=bZd5KmPx1oIzV0I&keytype=ref

NAR is one of the principal sources for research in genomics and esp.
biocomputing.

In this work we report on a novel Lisp-driven cDNA (~gene) assembly
technique that combines both genomic (dna) and EST (rna) information
to vastly improve the reliability of gene identification (in cDNA
assembly). In this application, Lisp (specifically, ACL) served as
both the scripting language, and, more importantly, as the core
computing engine, running a rather intricate recursive clustering
algorithm. This algorithm is the central contribution of this work. It
is described in more detail in this paper:

Jain, M, Holz, H, Shrager, J, Vallon, O, Hauser, C, Grossman, AR.
18th International
Conference on Pattern Recognition (ICPR'06), IEEE

Available here:

http://nostoc.stanford.edu/jeff/personal/vita/pubs/2006JainICpR.pdf


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.