Phylogenetic Footprinting and Consistent Sets of Local Aligments

The problem of constructing alternative local multiple sequence alignments from a collection of local pairwise alignments arises naturally in phylogenetic footprinting, a technique used to identify regulatory elements by comparative sequence analysis. Based on a theoretical discussion of the problem we devise an efficient heuristic and introduce the software tool tracker2 for this task. Tests on both biological and random data demonstrated the heuristic yields excellent results at very short runtimes.

[1]  Robert E. Tarjan,et al.  Depth-First Search and Linear Graph Algorithms , 1972, SIAM J. Comput..

[2]  Reinhardt Euler.  On a classification of independence systems , 1983, Z. Oper. Research.

[3]  Andreas Wilm,et al.  An enhanced RNA alignment benchmark for sequence alignment programs , 2006, Algorithms for Molecular Biology.

[4]  M. Blanchette,et al.  Discovery of regulatory elements by a computational method for phylogenetic footprinting. , 2002, Genome research.

[5]  Isaac Elias,et al.  Settling the Intractability of Multiple Alignment , 2003, ISAAC.

[6]  Sonja J. Prohaska,et al.  Surveying phylogenetic footprints in large gene clusters: applications to Hox cluster duplications. , 2004, Molecular phylogenetics and evolution.

[7]  Henry D. Shapiro,et al.  An Exact Characterization of Greedy Structures , 1993, IPCO.

[8]  D. Haussler,et al.  Article Identification and Characterization of Multi-Species Conserved Sequences , 2022 .

[9]  J. Stoye,et al.  Consistent Equivalence Relations: A Set-Theoretical Framework for Multiple Sequence Alignment , 1999 .

[10]  Paul Flicek,et al.  Optimising oligonucleotide array design for ChIP-on-chip , 2007, BMC Bioinformatics.

[11]  M. Gerstein,et al.  Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements , 2003, Journal of biology.

[12]  Steven J. M. Jones,et al.  Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. , 2006, Genome research.

[13]  Burkhard Morgenstern,et al.  DIALIGN: finding local similarities by multiple sequence alignment , 1998, Bioinform..

[14]  Alexander J. Hartemink,et al.  Finding regulatory DNA motifs using alignment-free evolutionary conservation information , 2010, Nucleic acids research.

[15]  D. Higgins,et al.  T-Coffee: A novel method for fast and accurate multiple sequence alignment. , 2000, Journal of molecular biology.

[16]  Erik van Nimwegen,et al.  Finding regulatory elements and regulatory motifs: a general probabilistic framework , 2007, BMC Bioinformatics.

[17]  Suhua Chang,et al.  i-GSEA4GWAS: a web server for identification of pathways/gene sets associated with traits by applying an improved gene set enrichment analysis to genome-wide association study , 2010, Nucleic Acids Res..

[18]  Burkhard Morgenstern,et al.  A min-cut algorithm for the consistency problem in multiple sequence alignment , 2010, Bioinform..

[19]  Wilfred W. Li,et al.  MEME: discovering and analyzing DNA and protein sequence motifs , 2006, Nucleic Acids Res..

[20]  Serafim Batzoglou,et al.  Eukaryotic regulatory element conservation analysis and identification using comparative genomics. , 2004, Genome research.

[21]  Erik van Nimwegen,et al.  PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny , 2005, PLoS Comput. Biol..