Extended Mode of Contig Viewer

Two PHP scripts get_viewer_contig_data.php and get_viewer_coordinates.php should be placed into defined web directories. Those PHP scripts interact with mySQL database and extract information from two tables. First table contains EST sequences. Second table contains data for splicing sites of Arabidopsis thaliana. Details about tables set up can be found at: CGPDB mySQL. Information about splicing sites for Arabidopsis genome was derived using Python GenBank Parser. Note, that drawing of splicing sites does not take into consideraration gaps on BLAST alignments. It means, if gaps are large, position(s) of introns may be slightly shifted to their actual position(s). BLAST reports for every sequence or contig also should be placed into pre-defined web directories. Path to those directories is embedded into the source code of Contig Viewer. Proper set up of scripts and database requires moderate level of experince in mySQL and PHP. Questions and comments are very welcome: akozik@atgc.org, Alexander Kozik.

Dataflow scheme at the extended mode:

last modified: February 15 2004