The D. melanogaster, A. gambiae, A. mellifera, H. virescens, B. mori, and A. aegypti olfactory and gustatory receptor sequences were downloaded from the genomic DNA archive database at the national center for biotechnology information (NCBI) (http://www.ncbi.nih.gov/blast/agtrace.html/).html/
In the genomic trace archive of the hemichordate Saccoglossus kowalevskii, with 7× coverage, we have used our Gene Family Finder program (see Methods) to computationally identify two orthologs.
Disc1 L100P was originally identified in one G1 progeny of several thousand screened for Disc1 mutants from a G1 male genomic DNA archive produced by breeding ENU-mutagenized C57BL/6 J males and untreated DBA/2JJcl females [ 24].
Close collaboration with other projects at the EBI including InterPro (4), the Database of Genomic Variants archive (DGVa) (5) and HGNC (6) ensures that Ensembl resources are integrated and available through other important bioinformatics resources.
Public databases such as the Sequence Read Archive SRAA) (6, 7), database of Genotypes and Phenotypes (dbGaP) (8), Single Nucleotide Polymorphism Database (dbSNP) (9), Database of Genomic Variants archive (DGVa) (10) and the Catalog Of Somatic Mutations In Cancer (COSMIC) (11) contain both raw sequencing data as well as various types of genomic variants, which can affect human biological function.
This result appears to be consistent with tBLASTn searches of the S. purpuratus genomic trace archive directly, in which 22 of 23 traces identified containing this ORF also have a stop codon at the same position [*QVDVYYHH.], suggesting that this stop codon is not a sequencing error.
The TblastN hits from the genomic trace archives were validated and grouped using subsequent blast analyses.
The resource center NBRP Medaka provides a screening system for the genomic DNA archives with high-resolution melting (HRM).
A bioinformatics pipeline, Gene Family Finder (GFF), was developed to facilitate the identification of gene-family members within genomic trace archives, and used to search for GATA genes from the hemichordate Saccoglossus kowalevskii (Additional File 5).
A medaka TILLING library has been established that consists of 5760 ENU mutagenized F1 fish (offspring from ENU-treated males crossed to wild-type females) and their genomic DNA archives.
