Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment.

By W. James Kent, Alan M. Zahler. Genome Research, 2000

298 citations recorded by the source corpus.

A new algorithm, WABA, was developed for doing large-scale alignments between genomic DNA of different species. WABA was used to align 8 million bases of Caenorhabditis briggsae genomic DNA against the entire 97-million-base Caenorhabditis elegans genome. The alignment, including C. briggsae homologs of 154 genetically characterized C. elegans genes and many times this number of largely uncharacterized ORFs, can be browsed and searched on the Web (http://www.cse.ucsc.edu/ approximately kent/intronerator). The alignment confirms that patterns of conservation can be useful in identifying regulatory regions and rarely expressed coding regions. Conserved regulatory elements can be identified inside coding exons by examining the level of divergence at the wobble position of codons. The alignment reveals a bimodal size distribution of syntenic regions. Over 250 introns are present in one species but not the other. The 3' and 5' intron splice sites have more similarity to each other in introns unique to one species than in C. elegans introns as a whole, suggesting a possible mechanism for intron removal.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9734dd7ec0f1ba778a06ab3d209314441ea6f0d8

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Citations in the corpus

The human genome browser at UCSC. (2002, background): “The code originated with a small script in the C programming language, which displayed a splicing diagram for a gene prediction from the nematode C. elegans (Kent and Zahler 2000).”
Mauve: multiple alignment of conserved genomic sequence with rearrangements. (2004, methodology): “Repeat analysis using tools such as Repeat Masker, REPuter (Kurtz et al. 2000), and FORRepeats (Lefebvre et al. 2003a) can help to further classify unaligned regions.”
GMAP: a genomic mapping and alignment program for mRNA and EST sequence (2005, background): “…strategy is found in a variety of programs, including those for genome–genome alignment (Chainet al., 2003; Morgenstern, 1999; Batzoglouet al., 2000; Kent and Zahler, 2000; Schwartzet al., 2000; Maet al., 2002; Brudnoet al., 2003a,b; Bray et al., 2003; Kalafuset al., 2004), and constitutes the…”
Hidden Markov Models and their Applications in Biological Sequence Analysis (2009, background): “We can also make the states emit two aligned symbols, instead of a single symbol, so that the resulting HMM simultaneously generates two related symbol sequences [3, 4, 26].”
The UCSC Genome Browser (2003, unknown): “The UCSC Genome Browser was originally developed as an alternative to ACeDB to examine RNA splicing for gene predictions in C. elegans (Kent and Zahler, 2000a).”
Comprehensive splice-site analysis using comparative genomics (2006, background): “C . elegans exhibits a shorter and more conserved PPT in the intronic portion, with a consensus sequence of TTTTCAGR, where AG is the terminus of the intron (72).”
Integrating genomic homology into gene structure prediction (2001, result): “Similarly, in a large-scale comparison between the nematodes Caenorhabditis briggsae and Caenorhabditis elegans Kent & Zahler (2000) found that rearrangements are common, occurring on average every 8.5 Kb.”
The evolution of spliceosomal introns: patterns, puzzles and progress (2006, background): “Alternatively, introns could be lost by (near) exact genomic deletio”
Survey of clustering algorithms (2005, background): “(WABA) [162], for aligning large-scale genomic sequences of different species, which employs a seven-state pairwise hidden Markov model [78] for more effective alignments.”
Current methods of gene prediction, their strengths and weaknesses. (2002, background): “Finally, several programs try to retrieve information on conservation or synteny between organisms from genomic alignments, as, for example, MUMmer (76), WABA (77), PipMaker (78) and DIALIGN (79).”
Adaptive seeds tame genomic sequence comparison. (2011, background): “Modern DNA comparison methods achieve increased sensitivity through the use of spaced seeds (Kent and Zahler 2000; Ma et al. 2002).”
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics (2003, methodology): “elegans genomes, we created whole-genome alignments of the two genomes at the nucleotide level using the WABA algorithm (Kent and Zahler 2000).”