This reports the protocol used to align the Rice_BAC features to Rice tigrv4-genome.
These Rice BACs are not used in the Rice genome assembly, that is why sometimes they are
referred to as the unmapped.
  
Sat Sep  3 01:18:55 2005


Source of Rice_BAC: Downloaded from genbank   

Alignment procedure details 
--------------------------- 

The 2kb front and back end of each of the 668 Rice BACs were extracted and mapped seperately to the Rice Genome. 
The mappings from the front end and back end were combined to generate the mappings for the whole BAC.
In this way, 551 Rice BACs were mapped to TIGR Version 4 rice genome.

The Alignment procedures for the front end and back end are listed below:
  
668 Rice_unmapped_BAC_front are aligned to Rice_Genome(TIGR Version 4) using blat with blat parameters -minScore=120 followed by PslReps with -singleHit. This was followed by a filtering procedure described below and applied in general to 'No filters' data sets.

Following is the final summary
# alignments : 701
# unique Features these remaining alignments represent: 578
% of total features these alignments represent : 86.53 %


668 Rice_unmapped_BAC_back are aligned to Rice_Genome(TIGR Version 4) using blat with blat parameters -minScore=120 followed by PslReps with -singleHit. This was followed by a filtering procedure described below and applied in general to 'No filters' data sets.

Following is the final summary
# alignments : 682
# unique Features these remaining alignments represent: 586
% of total features these alignments represent : 87.72 %