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Deposited research article

Isochores Merit the Prefix 'Iso'

Wentian Li¹ , Pedro Bernaola-Galvan², Pedro Carpena² and Jose L Oliver³

¹Center for Genomics and Human Genetics, North Shore - LIJ Research Institute, 350 Community Drive, Manhasset, NY 11030, USA

²Departmenta de Fisica Aplicada II, Universidad de Malaga, E-39071, Malaga, Spain

³Departmento de Genetica, Instituto de Biotechnologia, Universidad de Granada, E-18071 Granada, Spain

author email corresponding author email

Genome Biology 2002, 3:preprint0009.1-0009.15doi:10.1186/gb-2002-3-11-preprint0009

Published:	23 September 2002

This is the first version of this article to be made available publicly. A peer-reviewed and modified version is now available in full at Computational Biology and Chemistry 2003, 27:5-10

Subject areas: Bioinformatics, Genome Studies

Abstract

The isochore concept in human genome sequence was challenged in an analysis by the International Human Genome Sequencing Consortium (IHGSC). We argue here that a statement in IGHSC analysis concerning the existence of isochore is incorrect, because it had applied an inappropriate statistical test. To test the existence of isochores should be equivalent to a test of homogeneity of windowed GC%. The statistical test applied in the IHGSC's analysis, the binomial test, is however a test of a sequence being random on the base level. For testing the existence of isochore, or homogeneity in GC%, we propose to use another statistical test: the analysis of variance (ANOVA). It can be shown that DNA sequences that are rejected by binomial test may not be rejected by the ANOVA test.