Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs. Export

@article{citeulike:118735, abstract = {A data set of 77 genomic mouse/human gene pairs has been compiled from the EMBL nucleotide database, and their corresponding features determined. This set was used to analyze the degree of conservation of noncoding sequences between mouse and human. A new alignment algorithm was developed to cope with the fact that large parts of noncoding sequences are not alignable in a meaningful way because of genetic drift. This new algorithm, DNA Block Aligner (DBA), finds colinear-conserved blocks that are flanked by nonconserved sequences of varying lengths. The noncoding regions of the data set were aligned with DBA. The proportion of the noncoding regions covered by blocks >60\% identical was 36\% for upstream regions, 50\% for 5' UTRs, 23\% for introns, and 56\% for 3' UTRs. These blocks of high identity were more or less evenly distributed across the length of the features, except for upstream regions in which the first 100 bp upstream of the transcription start site was covered in up to 70\% of the gene pairs. This data set complements earlier sets on the basis of cDNA sequences and will be useful for further comparative studies. [This paper contains supplementary data that can be found at http://www.genome.org [corrected]].}, address = {The Sanger Centre, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. niclas.jareborg@cgr.ki.se}, author = {Jareborg, N. and Birney, E. and Durbin, R.}, citeulike-article-id = {118735}, citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/10508839}, citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=10508839}, issn = {1088-9051}, journal = {Genome Res}, keywords = {alignment, comparative\_genomics, conservation, ncrna}, month = {September}, number = {9}, pages = {815--824}, posted-at = {2009-01-08 06:55:54}, priority = {2}, title = {Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/10508839}, volume = {9}, year = {1999} }

TY - JOUR ID - citeulike:118735 L3 - citeulike-article-id:118735 N2 - A data set of 77 genomic mouse/human gene pairs has been compiled from the EMBL nucleotide database, and their corresponding features determined. This set was used to analyze the degree of conservation of noncoding sequences between mouse and human. A new alignment algorithm was developed to cope with the fact that large parts of noncoding sequences are not alignable in a meaningful way because of genetic drift. This new algorithm, DNA Block Aligner (DBA), finds colinear-conserved blocks that are flanked by nonconserved sequences of varying lengths. The noncoding regions of the data set were aligned with DBA. The proportion of the noncoding regions covered by blocks >60% identical was 36% for upstream regions, 50% for 5' UTRs, 23% for introns, and 56% for 3' UTRs. These blocks of high identity were more or less evenly distributed across the length of the features, except for upstream regions in which the first 100 bp upstream of the transcription start site was covered in up to 70% of the gene pairs. This data set complements earlier sets on the basis of cDNA sequences and will be useful for further comparative studies. [This paper contains supplementary data that can be found at http://www.genome.org [corrected]]. IS - 9 JF - Genome Res SN - 1088-9051 AD - The Sanger Centre, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. niclas.jareborg@cgr.ki.se EP - 824 TI - Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs. VL - 9 SP - 815 KW - alignment KW - comparative_genomics KW - conservation KW - ncrna AU - Jareborg, N AU - Birney, E AU - Durbin, R PY - 1999/09// UR - http://view.ncbi.nlm.nih.gov/pubmed/10508839 ER -