PMC:1698483 / 112088-114202 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1698483","sourcedb":"PMC","sourceid":"1698483","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1698483","text":"The pseudo-code for the complete EXMOTIF algorithm is shown in Figure 6. The program takes as inputs the set of sequences S={Si}i=1n MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBamrtHrhAL1wy0L2yHvtyaeHbnfgDOvwBHrxAJfwnaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaWaaeGaeaaakeaaimaacqWFse=ucqGH9aqpcqGG7bWEcqWGtbWudaWgaaWcbaGaemyAaKgabeaakiabc2ha9naaDaaaleaacqWGPbqAcqGH9aqpcqaIXaqmaeaacqWGUbGBaaaaaa@43EE@, the motif template T MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBamrtHrhAL1wy0L2yHvtyaeHbnfgDOvwBHrxAJfwnaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaWaaeGaeaaakeaaimaacqWFtepvaaa@3847@ = M1[l1, u1] ... [lk-1, uk-1] Mk, the quorum threshold q, the number of errors or IUPAC symbols allowed per simple motif e={ei}i=1k MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaaieqacqWFLbqzcqGH9aqpcqGG7bWEcqWGLbqzdaWgaaWcbaGaemyAaKgabeaakiabc2ha9naaDaaaleaacqWGPbqAcqGH9aqpcqaIXaqmaeaacqWGRbWAaaaaaa@39CC@, and the set of IUPAC symbols to use per simple motif, v={vi}i=1k MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaaieqacqWF2bGDcqGH9aqpcqGG7bWEcqWG2bGDdaWgaaWcbaGaemyAaKgabeaakiabc2ha9naaDaaaleaacqWGPbqAcqGH9aqpcqaIXaqmaeaacqWGRbWAaaaaaa@3A10@ (only for position specific substitutions). As outlined in Figure 6 EXMOTIF allows several different variations to motif extraction, as described above. These variations include, exact matching, position-specific substitutions via use of IUPAC symbols, arbitrary substitutions, and repeated motif identification.","tracks":[]}