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Explanation of parameters contained in the Global Match File. |
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| Parameter |
Description |
Intended use and comments |
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| 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. |
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Various indexes were developed in the Global Match File in order to characterize alignment quality between tomato target and matching potato counterparts. The most relevant parameters are listed above along with their intended use in terms of assessing alignment quality. | ||
Bagnaresi et al. BMC Genomics 2008 9:176 doi:10.1186/1471-2164-9-176 |
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