RT Journal
A1 Hirosawa, Makoto
A1 Ishikawa, Ken-ichi
A1 Nagase, Takahiro
A1 Ohara, Osamu
T1 Detection of Spurious Interruptions of Protein-Coding Regions in Cloned cDNA Sequences by GeneMark Analysis
JF Genome Research 
JO Genome Research 
YR 2000 
FD September 01 
VO 10 
IS 9 
SP 1333 
OP 1341 
DO 10.1101/gr.129500 
UL http://genome.cshlp.org/content/10/9/1333.abstract 
AB cDNA is an artificial copy of mRNA and, therefore, no cDNA can be completely free from suspicion of cloning errors. Because overlooking these cloning errors results in serious misinterpretation of cDNA sequences, development of an alerting system targeting spurious sequences in cloned cDNAs is an urgent requirement for massive cDNA sequence analysis. We describe here the application of a modified GeneMark program, originally designed for prokaryotic gene finding, for detection of artifacts in cDNA clones. This program serves to provide a warning when any spurious split of protein-coding regions is detected through statistical analysis of cDNA sequences based on Markov models. In this study, 817 cDNA sequences deposited in public databases by us were subjected to analysis using this alerting system to assess its sensitivity and specificity. The results indicated that any spurious split of protein-coding regions in cloned cDNAs could be sensitively detected and systematically revised by means of this system after the experimental validation of the alerts. Furthermore, this study offered us, for the first time, statistical data regarding the rates and types of errors causing protein-coding splits in cloned cDNAs obtained by conventional cloning methods.