By Glonek G.F., Solomon P.J.

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Additional resources for Factorial and time course designs for cDNA microarray experiments

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TTA|TTA|TTA …; (2) replace randomly some nucleotides in this stretch (generally, random insertions/deletions should also be taken into account). The resulting stretch can be defined as a sequence with hidden periodicities. The frequency of random replacements may be biased in the different sites of a repeat. For instance, if the random replacements occur only in the first and second positions, this would yield the patterns NNA|NNA|NNA…, where N is any nucleotide. The period p = 3 has proved to be typical of both genes and pseudogenes [34, 35].

Ortutay C, Vihinen M (2008) PseudoGeneQuest: service for identification of different pseudogene types in the human genome. BMC Bioinformatics 9:299 45. Khurana E, Lam HY, Cheng C, Carriero N, Cayting P, Gerstein MB (2010) Segmental duplications in the human genome reveal details of pseudogene formation. Nucleic Acids Res 38:6997–7007 46. Suyama M, Harrington E, Bork P, Torrents D (2006) Identification and analysis of genes and pseudogenes within duplicated regions in the human and mouse genomes.

Sechellia; (2) the yakuba complex, composed by D. teissieri (D.  santomea are the two other species in this complex); and (3) a complex represented by D. erecta and D. orena [76–79].  1. Alternative tree reconstruction methods implemented in the MEGA version 5 [67] yield identical topologies (data not shown).  1 is consistent with those derived from other genes as well as using entire genomes [80–84]. 1 Entropy Analysis Here we present the results of a comparative analysis of DNA sequences related to the functional gene Est-6 and the putative pseudogene ψEst-6 in four populations of Drosophila melanogaster (Zimbabwe, Spain, California, and Venezuela).

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Factorial and time course designs for cDNA microarray experiments by Glonek G.F., Solomon P.J.

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