Literature DB >> 17990505

Absent sequences: nullomers and primes.

Greg Hampikian1, Tim Andersen.   

Abstract

We describe a new publicly available algorithm for identifying absent sequences, and demonstrate its use by listing the smallest oligomers not found in the human genome (human "nullomers"), and those not found in any reported genome or GenBank sequence ("primes"). These absent sequences define the maximum set of potentially lethal oligomers. They also provide a rational basis for choosing artificial DNA sequences for molecular barcodes, show promise for species identification and environmental characterization based on absence, and identify potential targets for therapeutic intervention and suicide markers.

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Year:  2007        PMID: 17990505     DOI: 10.1142/9789812772435_0034

Source DB:  PubMed          Journal:  Pac Symp Biocomput        ISSN: 2335-6928


  19 in total

1.  Forbidden penta-peptides.

Authors:  Tamir Tuller; Benny Chor; Nathan Nelson
Journal:  Protein Sci       Date:  2007-10       Impact factor: 6.725

2.  Word-based characterization of promoters involved in human DNA repair pathways.

Authors:  Jens Lichtenberg; Edwin Jacox; Joshua D Welch; Kyle Kurz; Xiaoyu Liang; Mary Qu Yang; Frank Drews; Klaus Ecker; Stephen S Lee; Laura Elnitski; Lonnie R Welch
Journal:  BMC Genomics       Date:  2009-07-07       Impact factor: 3.969

3.  Efficient computation of absent words in genomic sequences.

Authors:  Julia Herold; Stefan Kurtz; Robert Giegerich
Journal:  BMC Bioinformatics       Date:  2008-03-26       Impact factor: 3.169

4.  Minimal absent words in prokaryotic and eukaryotic genomes.

Authors:  Sara P Garcia; Armando J Pinho; João M O S Rodrigues; Carlos A C Bastos; Paulo J S G Ferreira
Journal:  PLoS One       Date:  2011-01-31       Impact factor: 3.240

5.  Minimal absent words in four human genome assemblies.

Authors:  Sara P Garcia; Armando J Pinho
Journal:  PLoS One       Date:  2011-12-29       Impact factor: 3.240

6.  Metagenome fragment classification using N-mer frequency profiles.

Authors:  Gail Rosen; Elaine Garbarine; Diamantino Caseiro; Robi Polikar; Bahrad Sokhansanj
Journal:  Adv Bioinformatics       Date:  2008-11-16

7.  The word landscape of the non-coding segments of the Arabidopsis thaliana genome.

Authors:  Jens Lichtenberg; Alper Yilmaz; Joshua D Welch; Kyle Kurz; Xiaoyu Liang; Frank Drews; Klaus Ecker; Stephen S Lee; Matt Geisler; Erich Grotewold; Lonnie R Welch
Journal:  BMC Genomics       Date:  2009-10-08       Impact factor: 3.969

8.  Genomic DNA k-mer spectra: models and modalities.

Authors:  Benny Chor; David Horn; Nick Goldman; Yaron Levy; Tim Massingham
Journal:  Genome Biol       Date:  2009-10-08       Impact factor: 13.583

9.  Comparative analysis of DNA word abundances in four yeast genomes using a novel statistical background model.

Authors:  Ramkumar Hariharan; Reji Simon; M Radhakrishna Pillai; Todd D Taylor
Journal:  PLoS One       Date:  2013-03-05       Impact factor: 3.240

10.  A dictionary based informational genome analysis.

Authors:  Alberto Castellini; Giuditta Franco; Vincenzo Manca
Journal:  BMC Genomics       Date:  2012-09-17       Impact factor: 3.969

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