Table 1 Explanation of parameters contained in the Global Match File.
Parameter | Description | Intended use and comments |
|---|---|---|
TOMATO_AFFY_ID | Tomato Probeset #ID | Tomato Affymetrix probeset identification |
POTATO_EST | ID of aligning potato TA/EST | Potato TA/EST identification |
DESCRIPTION | TIGR TA annotation | Updated TIGR annotation of potato TA/EST |
%_ALIGN/TARG | Ratio between aligned portion of potato TA/EST against the total length of the tomato target (ALIGN_LENGTH/LENGTH_TOM)*100 | Rough alignment evaluation between the tomato target and potato TA/EST. Scores higher than 100% reveal gaps in the alignment. |
%_PERF_ALIGN | Corrected ratio between aligned portion of potato EST against the tomato target (%_ALIGN/TARG*%_IDENTITY)/100 | This improvement of %_ALIGN/TARG parameter is needed to get the percentage of the net alignment, thus hiding the effects of non-contiguous alignment regions. Scores of 100% mean that the entire length of the tomato target sequence is aligned. |
%_STOP_DIST | Ratio between the position of the last nucleotide aligned in the tomato target against the total length of the tomato target (LAST_POS_TOM/LENGTH_TOM)*100. | - Similar, lower than 100% values of %_PERF_ALIGN and %_STOP_DIST suggest alignment interruption due to an intervening 3' UTR (outside coding sequence) -Very different values of %_PERF_ALIGN and %_STOP_DIST suggest alignment interruption within coding sequence. |