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We describe a set of rules for naming chromosomes and identifying loci, genes, and alleles based on biological function, mutant phenotype, and sequence identity, and suggest ways of dealing with aliases (synonyms), sequence variants, and loci identified by multiple annotations of the genome assemblies available from various sources.
We selected the 36 most-annotated and featured species (Table 1) from eukaryotic genomic assemblies available in the NCBI GenBank [41].
There are also strong discrepancies between the WGS database and the assemblies available via genomicBLAST.
There are currently three different unannotated genome assemblies available in the wgs section at NCBI.
To identify the ribosomal gene repeat, assemblies available through VectorBase were queried with different sequences using its BLAST [ 13] server.
Reads were mapped to Xenopus tropicalis v4.1 and v7.1 assemblies (available on http://www.xenbase.org) [ 27] using Bowtie (http://bowtie-bio.sourceforge.net) [ 28, 29].
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The tBLASTx search of the Drosophilid sequence-assemblies available through FlyBase identified 188 serpin orthologues.
stephensi genome assembly available.
The database for these organisms is pre-draft assembly available in GenBank in late March ,2004.
We thank the Culex genome consortium for making the genome assembly available before publication.
The 14× assembly was the only assembly available at the time when the BARCBean6K_1 BeadChip was designed.
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