Bull Math Biol. 1992 Jul;54(4):521-36.

A local algorithm for DNA sequence alignment with inversions.

Source

Department of Mathematics, University of Southern California, Los Angeles 90089-1113.

Abstract

A dynamic programming algorithm to find all optimal alignments of DNA subsequences is described. The alignments use not only substitutions, insertions and deletions of nucleotides but also inversions (reversed complements) of substrings of the sequences. The inversion alignments themselves contain substitutions, insertions and deletions of nucleotides. We study the problem of alignment with non-intersecting inversions. To provide a computationally efficient algorithm we restrict candidate inversions to the K highest scoring inversions. An algorithm to find the J best non-intersecting alignments with inversions is also described. The new algorithm is applied to the regions of mitochondrial DNA of Drosophila yakuba and mouse coding for URF6 and cytochrome b and the inversion of the URF6 gene is found. The open problem of intersecting inversions is discussed.

PMID:: 1591531; [PubMed - indexed for MEDLINE]

Publication Types, MeSH Terms, Substances

Publication Types

MeSH Terms

Substances

LinkOut - more resources

Full Text Sources

Other Literature Sources

Molecular Biology Databases

FlyBase

Libraries

LinkOut Holdings

Supplemental Content

Save items

Related citations in PubMed

An efficient algorithm to locate all locally optimal alignments between two sequences allowing for gaps. [Comput Appl Biosci. 1993]
An efficient algorithm to locate all locally optimal alignments between two sequences allowing for gaps.
Barton GJ. Comput Appl Biosci. 1993 Dec; 9(6):729-34.
GATA: a graphic alignment tool for comparative sequence analysis. [BMC Bioinformatics. 2005]
GATA: a graphic alignment tool for comparative sequence analysis.
Nix DA, Eisen MB. BMC Bioinformatics. 2005 Jan 17; 6:9. Epub 2005 Jan 17.
Combining many multiple alignments in one improved alignment. [Bioinformatics. 1999]
Combining many multiple alignments in one improved alignment.
Bucka-Lassen K, Caprani O, Hein J. Bioinformatics. 1999 Feb; 15(2):122-30.
Optimal spaced seeds for homologous coding regions. [J Bioinform Comput Biol. 2004]
Optimal spaced seeds for homologous coding regions.
Brejová B, Brown DG, Vinar T. J Bioinform Comput Biol. 2004 Jan; 1(4):595-610.
Review The Drosophila mitochondrial genome. [Oxf Surv Eukaryot Genes. 1984]
Review The Drosophila mitochondrial genome.
Clary DO, Wolstenholme DR. Oxf Surv Eukaryot Genes. 1984; 1:1-35.

See reviews... See all...

Cited by 4 PubMed Central articles

Homoplastic microinversions and the avian tree of life. [BMC Evol Biol. 2011]
Homoplastic microinversions and the avian tree of life.
Braun EL, Kimball RT, Han KL, Iuhasz-Velez NR, Bonilla AJ, Chojnowski JL, Smith JV, Bowie RC, Braun MJ, Hackett SJ, et al. BMC Evol Biol. 2011 May 25; 11:141. Epub 2011 May 25.
AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision. [Bioinformatics. 2011]
AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision.
Abyzov A, Gerstein M. Bioinformatics. 2011 Mar 1; 27(5):595-603. Epub 2011 Jan 13.
Retro-MoRFs: Identifying Protein Binding Sites by Normal and Reverse Alignment and Intrinsic Disorder Prediction. [Int J Mol Sci. 2010]
Retro-MoRFs: Identifying Protein Binding Sites by Normal and Reverse Alignment and Intrinsic Disorder Prediction.
Xue B, Dunker AK, Uversky VN. Int J Mol Sci. 2010 Sep 29; 11(10):3725-47. Epub 2010 Sep 29.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Compound (MeSH Keyword)
PubChem chemical compound records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

A local algorithm for DNA sequence alignment with inversions.
A local algorithm for DNA sequence alignment with inversions.
Bull Math Biol. 1992 Jul ;54(4):521-36.

PubMed
Target organ damage and associated clinical conditions among Nigerians with trea...
Target organ damage and associated clinical conditions among Nigerians with treated hypertension.
Cardiovasc J S Afr. 2005 Mar-Apr ;16(2):89-93.

PubMed
Changes in levels of alcohol consumption: United States, 1983-1988.
Changes in levels of alcohol consumption: United States, 1983-1988.
Br J Addict. 1992 Apr ;87(4):643-8.

PubMed
Stress in the professional practice of oncology nurses.
Stress in the professional practice of oncology nurses.
Cancer Nurs. 2005 May-Jun ;28(3):187-92.

PubMed
Intrauterine diethyltoluamide exposure and fetal outcome.
Intrauterine diethyltoluamide exposure and fetal outcome.
Reprod Toxicol. 1992 ;6(2):175-6.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: