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No other filter was applied to the BLAST results before their insertion into the database.
Data processing and insertion into the database was performed using multiple purpose-tailored scripts in python and R (R Development Core Team, 2010).
GO terms were obtained from the GO website (http://geneontology.org) and associated genes were obtained through the UCSC website for insertion into the database.
In addition to the automation of the IQE method, we also present a combinatorial bandgap analysis which is semiautomatic, and requires users' monitoring and decision making prior to insertion into the database.
The data retrieval and compilation for MoccaDB has involved the following steps: (1) extraction of data from various sources (publications, public databases etc).; (2) development and testing of additional new markers in Rubiaceae species; (3) compilation, elimination of marker redundancy, BLAST annotation; (4) insertion into the database.
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This avoid the insertion of inconsistent data into the database and ensures quality.
The HT protocols are activated by insertion into programmed database queries and reports.
This way, insertions to the database must be locally encrypted before being sent to the server.
This also means that the data entered into the database are correct at the time of insertion.
The Drosophila gene disruption project aimed for isolation of insertions within genes, and pre-selection of the transgenes before deposition into the database might create some distribution bias.
The DNA sequences flanking the transposon, pUTminiTn5Km2 (Table 1), were analyzed by comparison with online databases (www.pseudomonas.com), and revealed a transposon insertion into the flgE (PA1080) gene, (Figure 1B), between nucleotide 1021 and 1022.
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