Reconsidering the significance of genomic word frequency

We propose that the distribution of DNA words in genomic sequences can be primarily characterized by a double Pareto-lognormal distribution, which explains lognormal and power-law features found across all known genomes. Such a distribution may be the result of completely random sequence evolution by duplication processes. The parametrization of genomic word frequencies allows for an assessment of significance for frequent or rare sequence motifs

In search of lost introns

Many fundamental questions concerning the emergence and subsequent evolution of eukaryotic exon-intron organization are still unsettled. Genome-scale comparative studies, which can shed light on crucial aspects of eukaryotic evolution, require adequate computational tools. We describe novel computational methods for studying spliceosomal intron evolution. Our goal is to give a reliable characterization of the dynamics of intron evolution. Our algorithmic innovations address the identification of orthologous introns, and the likelihood-based analysis of intron data. We discuss a compression method for the evaluation of the likelihood function, which is noteworthy for phylogenetic likelihood problems in general. We prove that after $O(nL)$ preprocessing time, subsequent evaluations take $O(nL/\log L)$ time almost surely in the Yule-Harding random model of $n$-taxon phylogenies, where $L$ is the input sequence length. We illustrate the practicality of our methods by compiling and analyzing a data set involving 18 eukaryotes, more than in any other study to date. The study yields the surprising result that ancestral eukaryotes were fairly intron-rich. For example, the bilaterian ancestor is estimated to have had more than 90% as many introns as vertebrates do now

Studia Litteraria

Németh G. Béla: Nagy Miklós hetvenedik évére p. 5-9. Tamás Attila: Petőfi Sándor időszemléletéről p. 9-19. D eb re czeni Attila: Remény nélküli boldogság (Petőfi költői versei) p. 19-33. Rácz István György: „Apokalipszis ma" (Vörösmarty Mihály: Előszó) p. 33-51. Csűrös Miklós: Pázmán lovag Gondolatok Arany „víg balladájáéról p. 51-59. Nyilasy Balázs: Arany János naiv regéje a teljességről: Rege a csodaszarvasról p. 59-67. S. Varga Pál: Egy új Komjáthy-kiadás körvonalai p. 67-101. Lőkös István: Látlelet a századvégről egy horvát regényben (J. Leskovar: Roskadozó kastélyok) p. 101-113. Imre László: „Műfajfejlődés" vagy „rendszercsere"? (Bevezetés egy irodalmi korszak vizsgálatához) p. 113-125. Szegedy-Maszák Mihály: Az összehasonlító irodalomtudomány időszerűsége p. 125-136. Resumé p. 136-139. Regiszter a Studia Litteraria megjelent számaihoz p. 139-145. Névmutató p. 145-147