Cattle Genome Database FAQ

• Less is more. The CGD uses simple text searching to generate the output from the index. It does not allow for several key words to be submitted but something similar can be achieved by entering fewer characters into the index, or only part of the word you are looking for. If you do enter several words the engine will search for a specific phrase and you have to get punctuation and spacing correct.
• No output means no match, not a broken pipeline. The best thing to do is to give the search tool less information. One of the main causes of failure to match is putting in the redundant zero in locus names.
• It does not have to be a locus name. In general, if you enter any word or sequence of characters and these are in the database you will receive output.
• Searching for genes on chromosomes is now easy. To get all the genes assigned to chromosome 1 type BTA 1. Note there are two spaces between BTA and the chromosome number for numbers 1 to 9 and the X and a single space for the others.
• A few specific shortcuts to illustrate what is possible
  • Enter CGD to find all the genes contained in this database. This trick has been expanded so that PHYS will pick up all physically mapped genes, LINK will pick up all genetically mapped genes and OUTL will pick up all genetically mapped genes generated on families other than the IBRP.
  • Enter CSSM to find all the CSSM loci. This works for all families of anonymous DNA markers as well as gene families. This is a quick way to generate a file of several hundred kilobytes so be judicious in your choice.
  • Enter D1S to find the anonymous loci on chromosome 1. This works for all chromosomes, although the D number list is not yet completed.
• The citations/contacts section is case sensitive. This was done to provide two kinds of searching on family names. The contacts are in UPPER case but the citations are in Mixed case the way names are usually written. This prevents citations appearing in contacts and usually prevents contacts appearing in citations.
• The publicly available map is between 3 to 6 months old. The latest map is only available to those who have provided genotypic data for the latest map.
• The loci at the bottom of the map figure cannot be ordered precisely. If the position of a locus cannot be defined with statistically significant odds (1000:1) then it is placed at the foot of the chromosome map figure with a distance given usually to the closest ordered locus.
• The new map format will have NON-framework loci placed in their most likely interval. Non-framework loci will have names in italics. The distances between loci will be made searcheable so the two point distances between pairs of interest will be directly obtained.

revised: 12 April 1999