Michael E Sparks (mespar1@iastate.edu)
4 November 2007

Following is a brief description of the currently available gthXML-tools:

1. GenomeThreader.rng.txt

   • The gthXML v1.2 grammar specification (reverse compatible with v1.0,v1.1 documents), in Clark and Makoto's RELAX NG language (https://relaxng.org/).
   • jing, a tool to validate gthXML documents relative to this schema, is available at https://www.thaiopensource.com/relaxng/jing.html.
   • The GenomeThreader program is available at https://genomethreader.org.

2. ToolSAQ.v1.0.tar.bz2

   • A Common Lisp environment for manipulating gthXML-conformant datasets.

3. GSQ2XML.pl

   • Script to retrofit GeneSeqer (https://bioinformatics.iastate.edu/cgi-bin/gs.cgi) plain text output to the gthXML v1.1 format.

4. gthxmlToGFF.py

   • Converts gthXML formatted spliced alignments to GFF3 format.
   • This patch can be applied to produce results in GFF2 format, instead.
   • Called ``XML2GFF.py" at the GenomeThreader site.

5. xGDBload_PgsFromgthxml.py

   • Converts spliced alignments to executable SQL statements for import to xGDB (https://sourceforge.net/projects/xgdb)

6. gthDB_make.sql

   • SQL-based database for storing the more important information contained in gthXML files. Deprecated, but usable.

7. load_data.gthDB.pl

   • Populates gthDB. Deprecated, but usable.