Identification of the coding region of Saccharomyces cerevisiae chromosome VI using the computer program GenMark.
We searched the nucleotide sequence of budding yeast Saccharomyces cerevisiae chromosome VI (270 kb) for candidate coding regions, using the computer program GenMark. One hundred and twenty-nine putative genes were identified, which is almost the same as the number of ORFs on this chromosome. Nineteen new putative genes were identified through the GenMark analysis. Most large ORFs were also correctly identified (87% of the predicted putative genes identified by the GenMark (110 of 127) matched the reported ORFs). The new coding regions were mostly small but they were distinguished from the more than 2000 ORFs identified by Genetyx. GenMark did not predict 17 ORFs that were over 300 bp long. As these ORFs include known genes, their sequence context may differ somewhat from that of typical yeast genes. These analyses revealed the high potential of GenMark to identify putative genes from numerous short ORFs and will produce information on the likelihood of their being actual genes.
Hagiwara
H
H
Laboratory of Cellular Physiology, Institute of Physical and Chemical Research (RIKEN), Ibaraki, Japan.
Naitou
M
M
Shibata
T
T
Hanaoka
F
F
Eki
T
T
Murakami
Y
Y
D001483:Base Sequence; D015825:Chromosomes, Fungal; D016208:Databases, Factual; D005800:Genes, Fungal / Q000235:genetics*; D008390:Markov Chains; D016366:Open Reading Frames / Q000235:genetics; D012331:RNA, Fungal / Q000032:analysis; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D017386:Sequence Homology, Amino Acid; D012984:Software
D012331:RNA, Fungal