The most similar protein for each sequence assembly was determined using the BLASTX algorithm as implemented with the BioEdit software, using the default criteria and a maximum E-value set at 0.001.
Peak alignment was performed using the default criteria.
Finally, the masked BESs were BLASTed against the databases of all organisms by using the discontiguous megablast program at NCBI using the default criteria.
The backward regression analyses were performed in SPSS v.15 and used the default criterion probability of F-to-remove > =.10.
6. GFF files can be filtered using the default filtering criteria supplied in a configuration file, or according to the user's preferences.
The Garli Web Service [ 59], functioning on the Lattice Project grid system [ 60], was used to execute 1000 nonparametric bootstrap replicates asynchronously in parallel using the default stopping criteria.
Blast2Go (B2G) was used at the default criterion to functionally annotated the contigs.
For the similarity search of the bprJ1 sequence, the program YASS was used on the web server [ 43] using the default parameters, except for the 'Hit criterion strategy', which was set on 'double hit'.
In addition, we also performed multivariate survival analysis using Cox's regression model (with classic prognostic predictors entered in a backward stepwise approach with the log-likelihood ratio (L-R) significance test, using the default values for entering and exclusion criteria) to evaluate the independent prognostic value of the studied indices (SMI, MAI, and AI) in addition to MNA and FTD.
However, with Connectivity Search, using all the default criteria settings (except with criteria 'A' set to '1', so that only ChEMBL data is retrieved) a total of 16 records are retrieved, as shown in Figure 2. The result set includes molecules such as CHEMBL10347 (Rauwolscine), a stereoisomer of Yohimbine.
