Alignment of whole genomes | RDL Research Database

Abstract

A new system for aligning whole genome sequences is described. Using an efficient data structure called a suffix tree, the system is able to rapidly align sequences containing millions of nucleotides. Its use is demonstrated on two strains of Mycoplasma tuberculosis, on two less similar species of Mycoplasma bacteria and on two syntenic sequences from human chromosome 12 and mouse chromosome 6. In each case it found an alignment of the input sequences, using between 30 s and 2 min of computation time. From the system output, information on single nucleotide changes, translocations and homologous genes can easily be extracted. Use of the algorithm should facilitate analysis of syntenic chromosomal regions, strain-to-strain comparisons, evolutionary comparisons and genomic duplications.

Keywords

BiologySyntenyGenomeGeneticsChromosomeComputational biologyGene

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Publication Info

Year: 1999
Type: article
Volume: 27
Issue: 11
Pages: 2369-2376
Citations: 914
Access: Closed

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APA Style

                            
                                
                                    Arthur L. Delcher, 
                                
                                    Simon Kasif, 
                                
                                    R. D. Fleischmann
                                
                                et al.
                            
                            (1999). 
                            Alignment of whole genomes. 
                            Nucleic Acids Research
                            , 27
                            (11)
                            , 2369-2376.
                            https://doi.org/10.1093/nar/27.11.2369
                        

Identifiers

DOI: 10.1093/nar/27.11.2369