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- MaMF abstract "MaMF, or Mammalian Motif Finder, is an algorithm for identifying motifs to which transcription factors bind.The algorithm takes as input a set of promoter sequences, and a motif width(w), and as output, produces a ranked list of 30 predicted motifs(each motif is defined by a set of N sequences, where N is a parameter).The algorithm firstly indexes each sub-sequence of length n, where n is a parameter around 4-6 base pairs, in each promoter, so they can be looked up efficiently. This index is then used to build a list of all pairs of sequences of length w, such that each sequence shares an n-mer, and each sequence forms an ungapped alignment with a substring of length w from the string of length 2w around the match, with a score exceeding a cut-off.The pairs of sequences are then scored. The scoring function favours pairs which are very similar, but disfavours sequences which are very common in the target genome. The 1000 highest scoring pairs are kept, and the others are discarded. Each of these 1000 'seed' motifs are then used to search iteratively search for further sequences of length which maximise the score(a greedy algorithm), until N sequences for that motif are reached.Very similar motifs are discarded, and the 30 highest scoring motifs are returned as output.".
- MaMF wikiPageID "4839372".
- MaMF wikiPageRevisionID "574508864".
- MaMF hasPhotoCollection MaMF.
- MaMF subject Category:Bioinformatics.
- MaMF subject Category:Search_algorithms.
- MaMF type Abstraction100002137.
- MaMF type Act100030358.
- MaMF type Activity100407535.
- MaMF type Algorithm105847438.
- MaMF type Event100029378.
- MaMF type Procedure101023820.
- MaMF type PsychologicalFeature100023100.
- MaMF type Rule105846932.
- MaMF type SearchAlgorithms.
- MaMF type YagoPermanentlyLocatedEntity.
- MaMF comment "MaMF, or Mammalian Motif Finder, is an algorithm for identifying motifs to which transcription factors bind.The algorithm takes as input a set of promoter sequences, and a motif width(w), and as output, produces a ranked list of 30 predicted motifs(each motif is defined by a set of N sequences, where N is a parameter).The algorithm firstly indexes each sub-sequence of length n, where n is a parameter around 4-6 base pairs, in each promoter, so they can be looked up efficiently.".
- MaMF label "MaMF".
- MaMF sameAs m.0cqclr.
- MaMF sameAs Q16335190.
- MaMF sameAs Q16335190.
- MaMF sameAs MaMF.
- MaMF wasDerivedFrom MaMF?oldid=574508864.
- MaMF isPrimaryTopicOf MaMF.