Once the PHAT outputs are organized into a cross-correlation matrix, in which each row represents a PHAT output, a false trajectory corresponding to the peaks may be present along the running time dimension.
In order to overcome the huge quantity of possible answers, the output is organized in a binary tree.
We reasoned that if dynamic changes occur in how the motor output is organized during the course of recovery, these would likely be reflected in corresponding changes in the relationships between physiological parameters and behavioral measures.
The output is organized into three tables and one figure: i) Table 1, the "Summary of Results" contains links to detailed information on analysis of regulons, TFBS, promoters, transcription terminators, RNA folding and motif analysis using MEME, ii) Table 2 and Table 3, "Files available for download", iii) Table 4, Combined results of the TFBS and regulon mining.
The overall procedure that led to the completion of the GrapeMiRNA web database involved the preparation of several parsers, scripts and accessory programs that allowed extracting relevant results from programs' outputs and organizing them in the database tables.
The source code necessary for the generation of output files is organized in three separate Perl modules.
The BLAST outputs were filtered and organized using a Perl script.
The paper is guided by the output of a workshop organized in May 2011 by the International Life Sciences Institute Europe (ILSI Europe) in which representatives from governmental bodies, industry and academia came together to discuss such challenges and consider how these may be met.
ViroBLAST was used to implement our Mnemiopsis BLAST tool, producing an organized, manageable output that is easy to parse and navigate.
The output from PILER was organized into families (all sequences with 95% and higher similarity) and superfamilies (sequences from two or more families that exhibited sequence similarity).
