Aligning multiple genomic sequences with the threaded blockset aligner.

By M. Blanchette, W. James Kent, C. Riemer, L. Elnitski, Arian F. A. Smit, Krishna M. Roskin, Robert Baertsch, Kate R. Rosenbloom, Hiram Clawson, Eric D. Green and 2 more. Genome Research, 2004

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We define a "threaded blockset," which is a novel generalization of the classic notion of a multiple alignment. A new computer program called TBA (for "threaded blockset aligner") builds a threaded blockset under the assumption that all matching segments occur in the same order and orientation in the given sequences; inversions and duplications are not addressed. TBA is designed to be appropriate for aligning many, but by no means all, megabase-sized regions of multiple mammalian genomes. The output of TBA can be projected onto any genome chosen as a reference, thus guaranteeing that different projections present consistent predictions of which genomic positions are orthologous. This capability is illustrated using a new visualization tool to view TBA-generated alignments of vertebrate Hox clusters from both the mammalian and fish perspectives. Experimental evaluation of alignment quality, using a program that simulates evolutionary change in genomic sequences, indicates that TBA is more accurate than earlier programs. To perform the dynamic-programming alignment step, TBA runs a stand-alone program called MULTIZ, which can be used to align highly rearranged or incompletely sequenced genomes. We describe our use of MULTIZ to produce the whole-genome multiple alignments at the Santa Cruz Genome Browser.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/384c6943777e950f56effaeb6f9a0bf614145718

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Citations in the corpus

The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes (2014, background): “BSR [28], Magic [29], Mavid [30], Mauve [31-33], MGA [34], M-GCAT [35], Mugsy [36], TBA [37], multi-LAGAN [38], PECAN [39]), multiple genome alignment remains a challenging task due to the prevalence of horizontal gene transfer [26,40], recombination, homoplasy, gene conversion, mobile genetic eleme”
Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution (2011, methodology): “…and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco and California Institute for Quantitative Biosciences, San Francisco, CA 94158, USA 5These authors contributed equally to this work *Correspondence: dbartel@wi.mit.edu DOI 10.1016/j.cell.2011.11.055”
Comparative genomics reveals insights into avian genome evolution and adaptation (2014, methodology): “2) (122), yielding 603Mb (including gaps) chicken-referenced alignments.”
Recent developments in the MAFFT multiple sequence alignment program (2008, neutral): “ABA [44] (for protein/DNA), ProDA [45] (for protein), TBA [46] (for genomic DNA) and MAUVE [47] (for genomic DNA) are available.”
PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans. (2008, background): “These rasi-like piRNAs interact with the MILI AGO, which is expressed in the same developmental stages ( Aravin et al., 2007 ).”
The UCSC Genome Browser database: update 2010 (2009, background): “About half of the organisms hosted in the browser include multiple sequence alignment (multiz) tracks (7).”
Ensembl comparative genomics resources (2016, methodology): “These include VISTA, which currently distributes a 5-way primate multiple alignment and the GenomeVISTA toolkit (57) and the UCSC Genome Browser with a variety of MultiZ alignments (58).”
Identification and Classification of Conserved RNA Secondary Structures in the Human Genome (2006, methodology): “We constructed a whole-genome alignment of the human [23], chimpanzee [24], mouse [25], rat [26], dog, chicken [27], zebra fish, and puffer fish [28] genomes using the MULTIZ program [13,29].”
Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals (2005, background): “The human sequence in each set was aligned to the other three mammalian genome”
Genome sequence, comparative analysis and haplotype structure of the domestic dog (2005, methodology): “All other comparative analyses were performed on BLASTZ/MULTIZ 111,112 genome-wide alignments obtained from the UCSC genome browser (http://genome.ucsc.edu), based on CanFam1.”
Alignment-free sequence comparison: benefits, applications, and tools (2017, methodology): “…(e.g., ClustalW [3], Muscle [4], MAFFT [5]), sequences ’ profile search programs (e.g., PSI-BLAST [1], HMMER/Pfam [6]), and whole-genome aligners (e.g., progressive Mauve [7], BLASTZ [8], TBA [9]); these tools became game-changers for anyone who wanted to assess the functions of genes and proteins.”
microRNA Target Predictions across Seven Drosophila Species and Comparison to Mammalian Targets (2005, methodology): “The following assemblies were used to construct the multiz alignments [31]: D.”