TY - JOUR
AU - Mironov, A. A.
AB - Motivation: Sequencing of complete eukaryotic genomes and largesyntenic fragments of genomes makes it possible to apply genomiccomparison for gene recognition.Results: This paper describes a spliced alignment algorithm thataligns candidate exon chains of two homologous genomic sequencefragments from different species. The algorithm is implemented inPro-Gen software. Unlike other algorithms, Pro-Gen does not assumeconservation of the exon–intron structure. Amino acidsequences obtained by the formal translation of candidate exons arealigned instead of nucleotide sequences, which allows for distantcomparisons. The algorithm was tested on a sample ofhuman–mammal (mouse), human–vertebrate (Xenopus) and human–invertebrate (Drosophila ) gene pairs.Surprisingly, the best results, 97–98% correlation between theactual and predicted genes, were obtained for more distantcomparisons, whereas the correlation on the human–mouse samplewas only 93%. The latter value increases to 95% if conservation ofthe exon–intron structure is assumed. This is caused by alarge amount of sequence conservation in non-coding regions of thehuman and mouse genes probably due to regulatoryelements.Availaility: Pro-Gen v. 3.0 is available to academicresearchers free of charge at http://www.anchorgen.com/pro_gen/pro_gen.html.Contact: misha@imb.imb.ac.ru*To whom correspondence should beaddressed.
TI - Gene recognition in eukaryotic DNA by comparison of genomic  sequences
JF - Bioinformatics
DO - 10.1093/bioinformatics/17.11.1011
DA - 2001-11-01
UR - https://www.deepdyve.com/lp/oxford-university-press/gene-recognition-in-eukaryotic-dna-by-comparison-of-genomic-sequences-Kzm8oIKIj8
SP - 1011
EP - 1018
VL - 17
IS - 11
DP - DeepDyve
ER -