The BioVelo and SAQP implementations are applicable to any DB built using Ocelot, and thus generalize beyond Pathway Tools DBs such as the BioCyc DBs.
DB builds an R* tree using the Java implementation freely available at [ 30] to index all of the trapezoids of M, and uses this data tree to identify the trapezoids that intersect a given trapezoid.
This SNP resource is freely accessible at the National Center for Biotechnology Information (NCBI) SNP database (NCBI db SNP build 132) as "reference SNPs (rsSNPs)" with detailed annotation in the rice genome.
The OsRpl6-1 and OsRpl6-2 genes are assigned to chromosomes (Chrs) 3 and 8 as loci Os03g0725000 and Os08g0484301, respectively, in the Rice Annotation Project Database (RAP-DB) Build 4 [ 21].
Among the 33 OsATG homologues, 23 were identified from RAP-DB build 5: OsATG1b, OsATG1c, OsATG3b, OsATG4b, OsATG5b, OsATG6a OsATG6ba, OsATG7b, OsATG8d OsATG8e, OsATG8f, OsATG9a, OsATG9b, OsATG13a OsATG13b, OsATG16b, OsATG18a OsATG18b, OsATG18c, OsATG18d, OsATG18e, OsandG18e, and OsATG18f.
Sequences homologous to the rice rpl6 gene were sought using the BLAST algorism in the National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov/ and the RAP-DB Build 4 http://rapdb.dna.affrc.go.jp/[ 21] databases and a rice rpl6 cDNA [GenBank accession no. AU184578] as the initial query.
Cassandra DB is built based on Amazon's Dynamo and Google BigTable [3].
For the increasing of peanut transcripts from Sanger and RNA-sequencing, a present largest database for Arachis species database (peanut DB) were built (http://bioinfolab.muohio.edu/txid3818v1/) [ 37].
DB (Design and build) and DBB (Design-bid-build) represent two different contracting forms in construction.
The ExCAPE-DB is built based on the AMBIT database and web application [19], enhanced with a free text search engine (Apache Solr [35]).
The server of LOTUS-DB was built with Linux Ubuntu Server 12.04, Apache 2, MySQL Server 5.5 and Python2.7.
