We are using genetically mapped probes and a reiterative hybridization methodology using overlapping probes
Clones within the contigs are selected for end-sequencing to determine minimally overlapping tiling paths for genome sequencing. Our reiterative hybridization approach allows an interpretation of clone order within a contig, and these interpretations are shown below.
-Data from MPI-MP is presented as BAC end hybdrization data, denoted by a Sp6 or a T7 at the end of a probe name.
-BACs in lower case or without a letter at the start of the clone name are data from MPI-MP exclusively. "-TA" after a probe name indicates the data are from MPI-MP exclusively.
(YACs, BACs, YAC and BAC ends, genetic markers) to construct hybridization based maps of regions of
Arabidopsis thaliana Chromosome one.
Because of our collaborations with other groups, mapping information can be different for the TAMU and IGF BAC libraries, thus the contigs are presented separately for each library.
-The order of BAC in the IGF contigs was determined by the program wprobeorder.
-We are attempting to integrate our hybridization data with the Washington University St. Louis/Cold Spring Harbor (WUStL/CSHL/CSHL) fingerprint database (fpc).
The BAC names are followed by the contig number assigned by the WUStL/CSHL fpc database. The WUStL/CSHL file used to assign contigs has not been updated by since May 1999, therefore, the contig number assigned to a BAC may not agree with the contig number presented on the sequencing page.
The BACs used as hybridization probes also have either a NA, NC or a number.
-"NA" indicates the BAC used as a hybridization probe was not in the WUStL/CSHL fpc database.
-"NC" indicates the BAC used as a hybridization probe was in the WUStL/CSHL fpc database, but did not have a statistically significant fingerprint match to the query BAC.
-A number after the BAC used as a hybridization probe is the statistical similiarity of the hybridization probe to the query BAC according to the WUStL/CSHL fpc database.
"-fp" following a BAC name indicates that the probe was used on a Southern blot to confirm hybridization data.
"-nr" after a BAC name indicates the probe BAC had a significant BLAST hit with the end sequence of the target BAC.
"-WU" following a BAC name indicates that the data is from the WUStL/CSHL fpc statistical output.
The numbers after a probe indicate recombinant inbred (RI) map position in cM.
A "~" preceding the number indicates the cM position is from a F2 map and the map position does not have as high a confidence value as a RI position.
The contigs reflect our best interpretation given the current mapping data. We welcome feedback about the usefulness of these contigs. We would also appreciate being informed of any errors or more optimal contig configurations.
Some of the contig files are large and may take some time to download.
More contigs will be added, and existing contigs will be updated, as warranted.