Promoter Sequence Analysis through No Gap Multiple Sequence Alignment of Motif Pairs

Keywords

Sequence logo, Motif (music), Sequence motif, Alignment-free sequence analysis, Computer science

References

• The promoter connectionThomas Werner — 2001
• Using MUMmer to Identify Similar Regions in Large Sequence SetsArthur L. Delcher, Steven L. Salzberg, Adam M. Phillippy — 2003
• Regulatory Modules Shared within Gene Classes as Well as Across Gene Classes Can Be Detected by the Same in Silico ApproachAndreas Klingenhoff, Kornelie Frech, Thomas Werner — 2002
• Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarityAndreas Klingenhoff, Kornelie Frech, Kerstin Quandt — 1999
• A survey of sequence alignment algorithms for next-generation sequencingHeng Li, Natalie Homer — 2010
• CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.Julie Thompson, Desmond G. Higgins, Toby J. Gibson — 1994
• Recent Evolutions of Multiple Sequence Alignment AlgorithmsCédric Notredame — 2007
• A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure predictionRenxiang Yan, Dong Xu, Jianyi Yang — 2013
• MUSCLE: multiple sequence alignment with high accuracy and high throughput.R. C. Edgar — 2004
• Replacing suffix trees with enhanced suffix arraysMohamed Abouelhoda, Stefan Kurtz, Enno Ohlebusch — 2004
• M-Coffee: combining multiple sequence alignment methods with T-CoffeeIain M. Wallace — 2006
• T-Coffee: A novel method for fast and accurate multiple sequence alignment.Cédric Notredame, Desmond G. Higgins, Jaap Heringa — 2000
• Fast and accurate short read alignment with Burrows–Wheeler transformHeng Li, Richard Durbin — 2009
• Theoretical and practical advances in genome halvingF. Collyn, L. Guy, M. Marceau — 2004
• Alignment Free Frequency Based Distance Measures for Promoter Sequence ComparisonKouser, Lalitha Rangarajan, D. Chandrashekar — 2015
• DIALIGN : multiple DNA and protein sequence alignment at BiBiServB. Morgenstern — 1996

Cited by

• Alignment free promoter sequence analysis using feature reduced cumulative distribution of motifsKahkashan Kouser, Lalitha Rangarajan — 2016
• Entropy Based Feature Selection for Lacunarity Analysis of Position Specific Motif Matrices of Promoter SequencesKahkashan Kouser, B. S. Rashmi, Lalitha Rangarajan — 2016
• Effective Feature Selection for Classification of Promoter SequencesKahkashan Kouser, P. G. Lavanya, Lalitha Rangarajan — 2016
• Statistical and Alignment Based Methods for Comparison of Non-Coding DNA SequencesKouser, Lalitha Rangarajan — 2015
• Feature Reduced Weighted Fuzzy Binarization for Histogram Comparison of Promoter SequencesK. Kouser, Lalitha Rangarajan — 2016
• Two-Step Verifications for Multi-instance Features Selection: A Machine Learning ApproachMd. Nawab Yousuf Ali, S. Nimmy — 2018

Related papers

• Multiple sequence alignment algorithms for the phylogenic analysis of chloroplast DNA.Adam Rumbold — 2004
• Consensus methods for DNA and protein sequence alignment.Michael S. Waterman, Robert Jones — 1990
• A tool for multiple sequence alignment.David J. Lipman, Stephen F. Altschul, John Kececioglu — 1989
• Multiple sequence alignment using evolutionary programmingKumar Chellapilla, Gary B. Fogel — 1999
• What are DNA sequence motifs?Patrik D’haeseleer — 2006
• A simulated annealing algorithm for finding consensus sequencesJonathan M. Keith, Peter D. Adams, Darryn Bryant — 2002
• An algorithm of multiple sequence alignment based on consensus sequence searched by simulated annealing and star alignmentDengfeng Yao, Minghu Jiang, Xu You — 2015
• HomologyPlot: Searching for homology to a family of proteins using a database of unique conserved patternsJ. M. R. Parker, Robert S. Hodges — 1994
• Multiple sequence alignment by consensus.Michael S. Waterman — 1986
• Embedding strategies for effective use of information from multiple sequence alignmentsSteven Henikoff, Jorja G. Henikoff — 1997