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These promoter sequences, and the plant motif database generated from the above website, were used as input to a program called Promoter Integration in Microarray Analysis (PRIMA v1.0) [43].
IPA is a knowledge database generated from the peer-reviewed scientific publications that enables discovery of biological networks in gene expression data, determining the functions most significant to those networks.
Sequences were analyzed by BLASTx against a local database generated from the data found [ 33, 38].
The database generated from the usage of the app can also answer new, dynamic and targeted questions.
Reference-set in each analysis was the complete microarray sequence Blast2GO database generated from the contig list.
The data were then queried against the amino acid substitution database generated from the BoNT/B1 Okra sequence.
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The database generated from this analysis allowed us to identify some transcripts, including several transcription factors, as novel candidates to regulate hypothalamic Trh gene expression or TRH neuron growth during the terminal phase of development.
Nanospray LC/MSE analysis of the whole venom of B. irregularis identified peptide evidence for 14 of the 45 (31.1%) putative toxin transcript clusters using a database generated from all of the unique transcripts (toxin and nontoxin) identified in the transcriptome.
Their importance is highlighted in our Fermentation Relevant Yeast Genes (FRYG) database, generated from literature and the fermentation-relevant phenotypic characteristics of null mutants described in the Saccharomyces Genome Database.
The BLAST program from the National Center for Biotechnology Information (NCBI) (http://www.ncbi.lm.nih.gov/BLAST), processed with the non-redundant sequences (nr) GenBank and the nucleotide database generated from Paracoccidioides spp. structural genome (http://www.broad.mit.edu/annotation/genome/paracoccidioides_brasiliensis/MultiHome.html), was used for the annotation.
The search was performed with a custom Saccharomyces Genome Database generated from Saccharomyces Genome Database (http://www.yeastgenome.org) containing 6,717 entries as of November 30th 2008.
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