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We would like to have high-throughput ways of identifying such TDFs.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We describe a method, GOGOT, which automatically detects the differentially expressed TDFs in a set of time-course electropherograms. Analysis by GOGOT is conducted as follows: correction of fragment lengths of TDFs, alignment of identical TDFs across different electropherograms, normalization of peak heights, and identification of differentially expressed TDFs using a special statistic. The output of the analysis is a highly reduced list of differentially expressed TDFs. Visual evaluation confirmed that the peak alignment was performed perfectly for the TDFs by virtue of the correction of peak fragment lengths before alignment in step 1. The validity of the automated ranking of TDFs by the special statistic was confirmed by the visual evaluation of a third party.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>GOGOT is useful for the automated detection of differentially expressed TDFs from cDNA-AFLP temporal electrophoretic data. The current algorithm may be applied to other electrophoretic data and temporal microarray data.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1748-7188-2-5","type":"journal-article","created":{"date-parts":[[2007,5,30]],"date-time":"2007-05-30T18:19:28Z","timestamp":1180549168000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["GOGOT: a method for the identification of differentially expressed fragments from cDNA-AFLP data"],"prefix":"10.1186","volume":"2","author":[{"given":"Koji","family":"Kadota","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ryoko","family":"Araki","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuji","family":"Nakai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Masumi","family":"Abe","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2007,5,30]]},"reference":[{"key":"30_CR1","doi-asserted-by":"publisher","first-page":"967","DOI":"10.1126\/science.1354393","volume":"257","author":"P Liang","year":"1992","unstructured":"Liang P, Pardee AB: Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. 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