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In this query, we first find all RNAi experiments that result in an Emb phenotype, then “Follow” these results to a corresponding set of Gene objects. Finally, we select a subset of the initial results based on chromosomal location. ” The “HERE” clause lets an additional condition be applied to the same tag. It is important to note that the query operators AND, OR, NOT, and HERE must be in all capitals; the remainder of the query can be in lowercase. This query will find all Variation objects between two genetic map points, and then selects a subset of polymorphisms based on the presence of the “SNP” tag.

For example, upstream regions of C. elegans genes could be rapidly aligned to a newly sequenced genome to search for candidate regulatory sequences. New methods have recently been developed to align multiple genomes simulataneously, such as MULTIZ (43). MULTIZ uses pairwise alignments between two genomes to guide subsequent alignments with other genomes. MULTIZ offers several advantages over pairwise alignments, including independence from the reference genome (C. elegans in the case of Caenorhabditis species).

1, E45. 3. Sternberg, P. , Waterston, R. , Eddy, S. , and Wilson, R. K. (2003) Genome sequence of additional Caenorhabditis species: enhancing the utility of C. elegans as a model organism. National Human Genome Research Institute. pdf Accessed: April 2006. 4. , Harris, T. , et al. (2005) WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. Nucleic Acids Res. 33, D383–D389. 5. Worm ENCODE Consortium (2005) Worm ENCODE White Paper. http://www. txt. Accessed: April 2006.

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