Pentamer vocabularies characterizing introns and intron-like intergenic tracts from Caenorhabditis elegans and Drosophila melanogaster

Gene

Volumn 304, Issue 1-2, 2003, Pages 183-192

  Bultrini, Emanuele ^a   Pizzi, Elisabetta ^a   Del Giudice, Paolo ^a   Frontali, Clara ^a  

^a ISTITUTO SUPERIORE DI SANITÀ   (Italy)

Author keywords

Caenorhabditis elegans; Drosophila melanogaster; Introns; Linguistic properties

Indexed keywords

NUCLEOTIDE; OLIGONUCLEOTIDE; SPACER DNA; UNTRANSLATED RNA;

ANALYSIS; ARTICLE; CAENORHABDITIS ELEGANS; CONTROLLED STUDY; CORRELATION ANALYSIS; DROSOPHILA MELANOGASTER; GENOME; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; RNA SPLICING; SPECIES COMPARISON; STATISTICAL ANALYSIS;

CAENORHABDITIS; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; MELANOGASTER;

EID: 0037472766     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(02)01206-4     Document Type: Article

References (17)

1. Baisnée P.-F., Hampson S., Baldi P. Why are complementary DNA strands symmetric? Bioinformatics. 18:2002;1021-1033.
2. Beckmann J.S., Brendel V., Trifonov E.N. Intervening sequences exhibit distinct vocabulary. J. Biomol. Struct. Dyn. 4:1986;391-400.
3. Bernardi G. The human genome: organisation and evolutionary history. Annu. Rev. Genet. 29:1995;445-476.
4. Bernardi G., Olofsson B., Filipski J., Zerial M., Salinas J., Cuny J., Meunier-Rotival M., Rodier F. The mosaic genome of warm-blooded vertebrates. Science. 228:1985;953-958.
5. Brendel V., Beckmann J.S., Trifonov E.N. Linguistic of nucleotide sequences: morphology and comparison of vocabularies. J. Biomol. Struct. Dyn. 4:1986;11-21.
6. Bussemaker H.J., Li H., Siggia E.D. Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis. Proc. Natl. Acad. Sci. USA. 97:2000;10096-10100.
7. Claverie J.-M., Bougueleret L. Heuristic informational analysis of sequences. Nucleic Acids Res. 14:1986;179-196.
8. Claverie J.-M., Sauvaget I., Bougueleret L. K-tuple frequency analysis, from intron/exon discrimination to T-cell epitope mapping. Methods Enzymol. 183:1990;237-252.
9. Coward E. Shufflet, shuffling sequences while conserving the k-let counts. Bioinformatics. 15:1999;1058-1059.
10. Fickett J.W., Tung C.-S. Assessment of protein coding measures. Nucleic Acids Res. 20:1992;6441-6450.
11. Forsdyke D.R., Mortimer J.R. Chargaff's legacy. Gene. 261:2000;127-137.
12. Frontali C., Pizzi E. Similarity in oligonucleotide usage in introns and intergenic regions contributes to long-range correlation in the C. elegans genome. Gene. 232:1999;87-95.
13. Gentles A.J., Karlin S. Genome-scale compositional comparisons in eukaryotes. Genome Res. 11:2001;540-546.
14. Guigò R., Fickett J.W. Distinctive sequence features in protein coding, genic non-coding and intergenic human DNA. J. Mol. Biol. 253:1995;51-60.
15. Lim L.P., Burge C.B. A computational analysis of sequence features involved in the recognition of short introns. Proc. Natl. Acad. Sci. USA. 98:2001;11193-11198.
16. Prabhu V.V. Symmetry observations in long nucleotide sequences. Nucleic Acids Res. 21:1993;2797-2800.
17. Saxonov S., Daizadeh I., Fedorov A., Gilbert W. An exhaustive database of protein-coding intron-containing genes. Nucleic Acids Res. 28:2000;185-190.