Multiple alignment using simulated annealing : branch point definition in human mRNA splicing

A method for the simultaneous alignment of a very large number of sequences using simulated annealing is presented. The total running time of the algorithm does not depend explicitly on the number of sequences treated. The method has been used for the simultaneous alignment of 1462 human intron sequ...

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Bibliographic Details
Published in:Nucleic acids research 1992-05, Vol.20 (10), p.2511-2516
Main Authors: LUKASHIN, A. V, ENGELBRECHT, J, BRUNAK, S
Format: Article
Language:English
Subjects:
Algorithms
annealing
Base Sequence
Biological and medical sciences
Consensus Sequence - genetics
Escherichia coli - genetics
Fundamental and applied biological sciences. Psychology
Humans
Introns - genetics
man
Molecular and cellular biology
Molecular genetics
Molecular Sequence Data
Monte Carlo Method
mRNA
Promoter Regions, Genetic - genetics
Repetitive Sequences, Nucleic Acid - genetics
RNA Splicing - genetics
RNA, Messenger - metabolism
Sequence Alignment - methods
splicing
Transcription. Transcription factor. Splicing. Rna processing
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Summary:A method for the simultaneous alignment of a very large number of sequences using simulated annealing is presented. The total running time of the algorithm does not depend explicitly on the number of sequences treated. The method has been used for the simultaneous alignment of 1462 human intron sequences upstream of the intron-exon boundary. The consensus sequence of the aligned set together with a calculation of the Shannon information clearly shows that several sequence motives are conserved: (i) a previously undetected guanosine rich region, (ii) the branch point and (iii) the polypyrimidine tract. The nucleotide frequencies at each position of the branch point consensus sequence qualitatively reproduce the frequencies of the experimentally determined branch points.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/20.10.2511