Biomaterial Database

Automatic intron detection in nuclear DNA sequences of Saccharomyces cerevisiae. 1995

A Kalogeropoulos

Institut de Génétique et Microbiologie, Centre Universitaire d'Orsay, France.

The goal of the present work is the construction of software (EXPLORA) which automatically detects Open Reading Frames (ORF), intron-containing or not, in the nuclear sequences of the yeast Saccharomyces cerevisiae. In order to detect introns within (or preceding) ORFs, one must define precise rules of how an intron is identified. These rules are described here. The software is able to detect correctly an intron-associated ORF in at least 88% of cases. We tested all yeast nuclear entries of the EMBL database with the software, and found, in addition to the known intron-associated ORFs, some others which may include an intron. Finally the software was applied to the DNA sequences of chromosomes III and XI, in which it detected eight new intron-associated ORFs.

UI	MeSH Term	Description	Entries
D007438	Introns	Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.	Intervening Sequences,Sequences, Intervening,Intervening Sequence,Intron,Sequence, Intervening
D004271	DNA, Fungal	Deoxyribonucleic acid that makes up the genetic material of fungi.	Fungal DNA
D001483	Base Sequence	The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.	DNA Sequence,Nucleotide Sequence,RNA Sequence,DNA Sequences,Base Sequences,Nucleotide Sequences,RNA Sequences,Sequence, Base,Sequence, DNA,Sequence, Nucleotide,Sequence, RNA,Sequences, Base,Sequences, DNA,Sequences, Nucleotide,Sequences, RNA
D012441	Saccharomyces cerevisiae	A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.	Baker's Yeast,Brewer's Yeast,Candida robusta,S. cerevisiae,Saccharomyces capensis,Saccharomyces italicus,Saccharomyces oviformis,Saccharomyces uvarum var. melibiosus,Yeast, Baker's,Yeast, Brewer's,Baker Yeast,S cerevisiae,Baker's Yeasts,Yeast, Baker
D015825	Chromosomes, Fungal	Structures within the nucleus of fungal cells consisting of or containing DNA, which carry genetic information essential to the cell.	Chromosome, Fungal,Fungal Chromosome,Fungal Chromosomes
D016366	Open Reading Frames	A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).	ORFs,Protein Coding Region,Small Open Reading Frame,Small Open Reading Frames,sORF,Unassigned Reading Frame,Unassigned Reading Frames,Unidentified Reading Frame,Coding Region, Protein,Frame, Unidentified Reading,ORF,Open Reading Frame,Protein Coding Regions,Reading Frame, Open,Reading Frame, Unassigned,Reading Frame, Unidentified,Region, Protein Coding,Unidentified Reading Frames