Biomaterial Database

Inferring genes from open reading frames. 1994

J W Fickett

Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, NM 87545.

One expects that in DNA without protein coding function, stop codons (which constitute three of the 64 possible codons) should occur frequently in all reading frames, and that a long open reading frame (ORF) can be interpreted as a sign for the existence of a gene. We make a beginning on introducing quantitative measures of confidence into this inference--taking Saccharomyces cerevisiae as a sample case--and show that some common assumptions can reasonably be questioned. In particular we show that statistical support for the biological function of shorter ORFs listed as putative genes in recent papers is in fact very weak. This is an issue of practical as well as theoretical interest, since researching the function of a putative gene is difficult and expensive.

UI	MeSH Term	Description	Entries
D008957	Models, Genetic	Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.	Genetic Models,Genetic Model,Model, Genetic
D004271	DNA, Fungal	Deoxyribonucleic acid that makes up the genetic material of fungi.	Fungal DNA
D005796	Genes	A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.	Cistron,Gene,Genetic Materials,Cistrons,Genetic Material,Material, Genetic,Materials, Genetic
D005800	Genes, Fungal	The functional hereditary units of FUNGI.	Fungal Genes,Fungal Gene,Gene, Fungal
D001482	Base Composition	The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.	Base Ratio,G+C Composition,Guanine + Cytosine Composition,G+C Content,GC Composition,GC Content,Guanine + Cytosine Content,Base Compositions,Base Ratios,Composition, Base,Composition, G+C,Composition, GC,Compositions, Base,Compositions, G+C,Compositions, GC,Content, G+C,Content, GC,Contents, G+C,Contents, GC,G+C Compositions,G+C Contents,GC Compositions,GC Contents,Ratio, Base,Ratios, Base
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
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
D018244	Chromosomes, Artificial, Yeast	Chromosomes in which fragments of exogenous DNA ranging in length up to several hundred kilobase pairs have been cloned into yeast through ligation to vector sequences. These artificial chromosomes are used extensively in molecular biology for the construction of comprehensive genomic libraries of higher organisms.	Artificial Chromosomes, Yeast,Yeast Artificial Chromosomes,Chromosomes, Yeast Artificial,YAC (Chromosome),YACs (Chromosomes),Artificial Chromosome, Yeast,Chromosome, Yeast Artificial,Yeast Artificial Chromosome