Literature DB >> 12490463

OWEN: aligning long collinear regions of genomes.

Aleksey Y Ogurtsov1, Mikhail A Roytberg, Svetlana A Shabalina, Alexey S Kondrashov.   

Abstract

OWEN is an interactive tool for aligning two long DNA sequences that represents similarity between them by a chain of collinear local similarities. OWEN employs several methods for constructing and editing local similarities and for resolving conflicts between them. Alignments of sequences of lengths over 10(6) can often be produced in minutes. OWEN requires memory below 20 L, where L is the sum of lengths of the compared sequences.

Mesh：

Year:  2002        PMID： 12490463     DOI： 10.1093/bioinformatics/18.12.1703

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  30 in total

1.  Indel-based evolutionary distance and mouse-human divergence.

Authors:  Aleksey Y Ogurtsov; Shamil Sunyaev; Alexey S Kondrashov
Journal:  Genome Res       Date:  2004-08       Impact factor: 9.043

2.  Widespread positive selection in synonymous sites of mammalian genes.

Authors:  Alissa M Resch; Liran Carmel; Leonardo Mariño-Ramírez; Aleksey Y Ogurtsov; Svetlana A Shabalina; Igor B Rogozin; Eugene V Koonin
Journal:  Mol Biol Evol       Date:  2007-05-23       Impact factor: 16.240

3.  Rapid repetitive element-mediated expansion of piRNA clusters in mammalian evolution.

Authors:  Raquel Assis; Alexey S Kondrashov
Journal:  Proc Natl Acad Sci U S A       Date:  2009-04-08       Impact factor: 11.205

4.  Complete genome sequence of Courdo11 virus, a member of the family Mimiviridae.

Authors:  Niyaz Yoosuf; Isabelle Pagnier; Ghislain Fournous; Catherine Robert; Bernard La Scola; Didier Raoult; Philippe Colson
Journal:  Virus Genes       Date:  2013-12-01       Impact factor: 2.332

5.  Prosurvival long noncoding RNA PINCR regulates a subset of p53 targets in human colorectal cancer cells by binding to Matrin 3.

Authors:  Ritu Chaudhary; Berkley Gryder; Wendy S Woods; Murugan Subramanian; Matthew F Jones; Xiao Ling Li; Lisa M Jenkins; Svetlana A Shabalina; Min Mo; Mary Dasso; Yuan Yang; Lalage M Wakefield; Yuelin Zhu; Susan M Frier; Branden S Moriarity; Kannanganattu V Prasanth; Pablo Perez-Pinera; Ashish Lal
Journal:  Elife       Date:  2017-06-05       Impact factor: 8.140

6.  Continuing evolution of Burkholderia mallei through genome reduction and large-scale rearrangements.

Authors:  Liliana Losada; Catherine M Ronning; David DeShazer; Donald Woods; Natalie Fedorova; H Stanley Kim; Svetlana A Shabalina; Talima R Pearson; Lauren Brinkac; Patrick Tan; Tannistha Nandi; Jonathan Crabtree; Jonathan Badger; Steve Beckstrom-Sternberg; Muhammad Saqib; Steven E Schutzer; Paul Keim; William C Nierman
Journal:  Genome Biol Evol       Date:  2010-01-22       Impact factor: 3.416

7.  progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement.

Authors:  Aaron E Darling; Bob Mau; Nicole T Perna
Journal:  PLoS One       Date:  2010-06-25       Impact factor: 3.240

8.  Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae.

Authors:  Eugene Kolker; Kira S Makarova; Svetlana Shabalina; Alex F Picone; Samuel Purvine; Ted Holzman; Tim Cherny; David Armbruster; Robert S Munson; Grigory Kolesov; Dmitrij Frishman; Michael Y Galperin
Journal:  Nucleic Acids Res       Date:  2004-04-30       Impact factor: 16.971

9.  Properties of non-coding DNA and identification of putative cis-regulatory elements in Theileria parva.

Authors:  Xiang Guo; Joana C Silva
Journal:  BMC Genomics       Date:  2008-12-03       Impact factor: 3.969

10.  Evolution of alternative and constitutive regions of mammalian 5'UTRs.

Authors:  Alissa M Resch; Aleksey Y Ogurtsov; Igor B Rogozin; Svetlana A Shabalina; Eugene V Koonin
Journal:  BMC Genomics       Date:  2009-04-16       Impact factor: 3.969
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.