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arXiv:1002.0065q-bio.BM

Automated DNA Motif Discovery

W. B. Langdon, Olivia Sanchez Graillet, A. P. Harrison

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Abstract

Ensembl's human non-coding and protein coding genes are used to automatically find DNA pattern motifs. The Backus-Naur form (BNF) grammar for regular expressions (RE) is used by genetic programming to ensure the generated strings are legal. The evolved motif suggests the presence of Thymine followed by one or more Adenines etc. early in transcripts indicate a non-protein coding gene. Keywords: pseudogene, short and microRNAs, non-coding transcripts, systems biology, machine learning, Bioinformatics, motif, regular expression, strongly typed genetic programming, context-free grammar.

arXiv comments
12 pages, 2 figures
Journal reference
DOI
Subjects
q-bio.BMBiomolecules q-bio.GNGenomics

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  1. Ask HN: How to find first users for niche ideas? 1 comment

    • University of Pennsylvania has some projects that include public providing help with genomic/epigenetic research related to given topic descripition[0]. (using l-systems & bnf[5][8][9] format as way to encode/handle dna sequences [1][2][3][4][6][7]) Example/demo of topic : [10]…

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