Linking to GALA

GALA is coordinate based -- all annotations are associated with chromosome start and stop points in a particular genome assembly or "freeze". The Add user ranges feature enables a user to add an arbitrary list of such ranges (e.g., results from separate research) as a "query" on his/her History page in order to combine them with other GALA queries or to utilize GALA's output features for this data. This can also be achieved automatically from other databases and web sites by using a specially formatted link, as follows.

Start with the base URL
    http://gala.cse.psu.edu/cgi-bin/gala_FREEZE?mode=Add+user+ranges&
where FREEZE is replaced by the assembly freeze that the range coordinates are based upon. The freeze should be specified as hg16 for the Human July 2003 freeze, mm4 for the Mouse Oct 2003 freeze, etc. (Note that users have a separate History page for each freeze, because it does not make sense to blindly combine query results whose coordinates are specified with respect to different freezes.)

Next, the list of ranges can be specified in two different ways.

1. For short lists, it is convenient to put the ranges directly into the URL. Add
       usrfile4=LIST_OF_RANGES
   to the base URL, where LIST_OF_RANGES consists of one or more ranges in the format chrN:START-STOP (no spaces allowed in URLs). If there are multiple ranges, they should be separated by '+' characters.

2. Another option that works well for long lists is to specify the URL of a BED-formatted file containing the ranges. The BED file format is described at UCSC Genome Browser: Custom tracks. In this format, "track" lines are used to divide the list into several queries and to specify a description for each query on the History page. If track lines are omitted, GALA's default is to put all of the ranges into one query with the generic description "user ranges". The URL of the BED file is sent to GALA by adding
       usrfile3=http://www.whereever.org/xxx/yyy.bed
   to the base URL above.

Lastly, you can specify an optional description for the query by appending
    &desc=description+goes+here
where "description+goes+here" must be URL-encoded (e.g. spaces replaced with '+'). This will override any descriptions in a BED file's track lines.

Example URLs:
http://gala.cse.psu.edu/cgi-bin/gala_hg16?mode=Add+user+ranges&usrfile4=chr11:5,210,000-5,285,000+chr16:142,000-172,000&desc=hemoglobin+clusters
http://gala.cse.psu.edu/cgi-bin/gala_rn3?mode=Add+user+ranges&usrfile3=http://www.bx.psu.edu/~giardine/GALA_example/rat_genes_near_hbb.bed