Found BACs

This program will display all BACs that have one or more overgos. The best use of this program is to find BACs that have two or more overgos within 120 Kbases. Those parameters would find BACs that correspond to the Nipponbare genome.

This program will take a long time (minutes) to run.If you get a server timeout error then see Brian or Rick.

Rice chromosome or project:	1 3 10 soybean soymap All
Filter:
Plates:	All 21 only 22 to 45 105 to 120 200 to 230
Limit overgos to:	Unambigiously known Potentially ambigious
Clone limits:	All Non-weak Strong only Look for 3rd dimensional?
Minimum number of overgo matches required:	1 2 3 4 5 6 7 8 9
Maximum distance between overgos in Kbases:	40 60 80 100 120 150 200 300 400 Unlimited
Text output format:	CSV (comma seperated) No output Web
Include rough graph of which overgos are on BACs?	No Yes, sort alphabetically Yes, sort by position
... graphing modifiers:	Collapse graph(s)? Continuous line? Inverse stars? Limit overgos?
Include graph of how many BACs match each overgo?	Yes
Include detailed overgo information?	Absolute position Name Plate, row, column
List BACs that do not fit parameters?	Ambigious Overgo count Distance
List debugging information?	Yes Delete bad plate 21 data? Nipponbare info

Help

Chromosome: For chromosome 1 then the "22 to 45" plate option should be choosen. This is because the other plate (21) does not have very good data. For the other rice chromosomes and for the soybean project using "All" plates will select just thier plates. Also make sure to choose the right filter for the project.
Plates: Because plate #21 was created with less restrictive overgos and because the overgos were closely spaced it will be hard to find unambigous overgos when using this plate.Therefore using plates #22 through #45 is recommended for chromosome 1.
Limit to: In general it is best to find unambigious overgos -- that is, the exact overgo that is presumed to match the BAC. However sometimes, especially with plate #21, it is very hard to find completely unambigious overgos and so you may wish to have a simple count of the minimum possible overgos. This is the "ambigious" option.
Clone limits: During scoring clones can be marked as weak, strong or unmarked. "All" uses all clones while non-weak uses clones marked as "strong" or those which are unmarked. The "3rd dimensional" question is will only use clones that are found in a 3-D intersection of pools. Warning: Both of these options will potentially eliminate a lot of valuable data and are highly sensitive to how well the hybs are scored. I.E., what one scorer considers "weak" may not be the same for another scorer. Likewise, if a scorer does a poor job on a given hyb (or the hyb itself is of low quality) then relying on the hyb to provide 3rd dimensional information can cause problems.
Detailed information: The "name" option will print out the names of the exact overgos found on the BAC (unambigious or best guess options) or the potential overgos (ambigious option.) The "position" option will print out the plate, row and column information
CSV format: Unless imported into the Excel with care then BAC names will sometimes be seen as exponent instead as text.
Graph: This will present a visual graph of how which overgos match the BAC. The graph uses one column per overgo and thus is not an accurate representation of the distance between overgos. Only BACs with unambigious or best guess overgos can be graphed. The graph may look very ugly if all 1700+ overgos are used thus it might be better to use this on a single plate such as #21. Graph is not compatible with CSV format.
Debugging information: This is only good for the software developers and, for most people, should be left unchecked.

Note: This program will take a couple of minutes to run. Your web browser may not give any indication that the program is actually running. Thus wait for a while after pressing the "submit" button before giving up in disgust.