Abstract
High-throughput DNA sequencing has produced a large number of closed and well annotated genomes. As the focus from whole genome sequencing and assembly moves towards resequencing, variant data is becoming more accessible and large quantities of polymorphisms are being detected. An easy-to-use tool for quickly assessing the potential importance of these discovered variants becomes ever important. Written in Perl, the VariantClassifier receives a list of polymorphisms and genome annotation, and generates a hierarchically-structured classification for each variant. Depending on the available annotation, the VariantClassifier may assign each polymorphism to a large variety of feature types, such as intergenic or genic; upstream promoter region, intronic region, exonic region or downstream transcript region; 5' splice site or 3' splice site; 5' untranslated region (UTR), 3' UTR or coding sequence (CDS); impacted protein domain; substitution, insertion or deletion; synonymous or non-synonymous; conserved or unconserved; and frameshift or amino acid insertion or deletion (indel). If applicable, the truncated or altered protein sequence is also predicted. For organisms with annotation maintained at Ensembl, a software application for d...Continue Reading
References
Nov 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·S Henikoff, J G Henikoff
Jan 11, 2000·Nucleic Acids Research·S T SherryK Sirotkin
May 5, 2001·Genome Research·P C Ng, S Henikoff
Dec 26, 2001·Nucleic Acids Research·Alex BatemanErik L L Sonnhammer
Aug 2, 2005·Nature·Marcel MarguliesJonathan M Rothberg
Dec 7, 2006·Nucleic Acids Research·T J P HubbardE Birney
Sep 7, 2007·PLoS Biology·Samuel LevyJ Craig Venter
Aug 16, 2008·PLoS Genetics·Pauline C NgJ Craig Venter
Nov 7, 2008·Nature·David R BentleyAnthony J Smith
Citations
Sep 24, 2013·Nature Genetics·Silvia CappelloStephen P Robertson
Nov 26, 2011·Genome Biology and Evolution·Laura E Williams, Jennifer J Wernegreen
Mar 12, 2013·Genome Biology and Evolution·Laura E Williams, Jennifer J Wernegreen
Jun 13, 2012·Nucleic Acids Research·Ngak-Leng SimPauline C Ng
Jan 17, 2012·BMC Research Notes·Qiang HuSong Liu
Sep 16, 2011·Genome Biology·Zippora BrownsteinKaren B Avraham
Jan 28, 2014·PloS One·Edvin KarlssonKerstin Myrtennäs
Mar 14, 2013·The EMBO Journal·Reza SharifiIvan Ahel
Sep 30, 2015·Nature·Seema S LakdawalaKanta Subbarao
Aug 11, 2015·Nature·Ronen DurstSusan A Slaugenhaupt
Jul 4, 2012·Mobile Genetic Elements·Casey M Bergman
May 14, 2011·American Journal of Human Genetics·Laura SouthgateRichard C Trembath
Jan 31, 2012·American Journal of Human Genetics·Pia OstergaardSteve Jeffery
Dec 12, 2012·Nature Genetics·Thomas CullupHeinz Jungbluth