About: MaMF     Goto   Sponge   NotDistinct   Permalink

An Entity of Type : yago:Rule105846932, within Data Space : dbpedia.demo.openlinksw.com associated with source document(s)
QRcode icon
http://dbpedia.demo.openlinksw.com/describe/?url=http%3A%2F%2Fdbpedia.org%2Fresource%2FMaMF

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). Very similar motifs are discarded, and the 30 highest scoring motifs are returned as output.

AttributesValues
rdf:type
rdfs:label
  • MaMF (en)
rdfs: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). Very similar motifs are discarded, and the 30 highest scoring motifs are returned as output. (en)
dcterms:subject
Wikipage page ID
Wikipage revision ID
Link from a Wikipage to another Wikipage
sameAs
dbp:wikiPageUsesTemplate
has 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. (en)
prov:wasDerivedFrom
page length (characters) of wiki page
foaf:isPrimaryTopicOf
is Link from a Wikipage to another Wikipage of
is foaf:primaryTopic of
Faceted Search & Find service v1.17_git139 as of Feb 29 2024


Alternative Linked Data Documents: ODE     Content Formats:   [cxml] [csv]     RDF   [text] [turtle] [ld+json] [rdf+json] [rdf+xml]     ODATA   [atom+xml] [odata+json]     Microdata   [microdata+json] [html]    About   
This material is Open Knowledge   W3C Semantic Web Technology [RDF Data] Valid XHTML + RDFa
OpenLink Virtuoso version 08.03.3330 as of Mar 19 2024, on Linux (x86_64-generic-linux-glibc212), Single-Server Edition (378 GB total memory, 59 GB memory in use)
Data on this page belongs to its respective rights holders.
Virtuoso Faceted Browser Copyright © 2009-2024 OpenLink Software