Dragon gene start finder: an advanced system for finding approximate locations of the start of gene transcriptional units.
We present an advanced system for recognition of gene starts in mammalian genomes. The system makes predictions of gene start location by combining information about CpG islands, transcription start sites (TSSs), and signals downstream of the predicted TSSs. The system aims at predicting a region that contains the gene start or is in its proximity. Evaluation on human chromosomes 4, 21, and 22 resulted in Se of over 65% and in a ppv of approximately 78%. The system makes on average one prediction per 177000 nucleotides on the human genome, as judged by the results on chromosome 21. Comparison of abilities to predict TSS with the two other systems on human chromosomes 4, 21, and 22 reveals that our system has superior accuracy and overall provides the most confident predictions.
Bajic
Vladimir B
VB
Knowledge Extraction Lab, Institute for Infocomm Research, Singapore 119613. bajicv@i2r.a-star.edu
Seah
Seng Hong
SH
D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods; D002891:Chromosomes, Human, Pair 21 / Q000235:genetics; D002892:Chromosomes, Human, Pair 22 / Q000235:genetics; D002894:Chromosomes, Human, Pair 4 / Q000235:genetics; D030541:Databases, Genetic; D015894:Genome, Human; D006801:Humans; D011237:Predictive Value of Tests; D012984:Software; D024363:Transcription Initiation Site; D014158:Transcription, Genetic / Q000235:genetics