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Aligns the given motifs against the DNA sequencies. This component supports IUPAC nucleotide codes in input sequences.

Version 1.7.1
Bundle microarray
Categories Annotation Sequence Motif
Authors Marko Laakso (Marko.Laakso@Helsinki.FI), Erkka Valo (erkka.valo@helsinki.fi)
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Requires Asser.jar (jar)
Source files component.xml
Usage Example with default values


Name Type Mandatory Description
motifs MotifSet Mandatory A set of motifs to be used
sequence FASTA Mandatory A list of sequencies to be compared against the motifs
seqSelection IDList Optional A list of sequence identifiers to be used from the original sequence file
bgIn MotifSet Optional Primary source of the backgroung frequencies of the nucleotides. This set should consist of a single motif with exacly one locus. Background parameter is used if this input is not available.
exclude IDList Optional A list of motif names to be excluded although included into motifs input


Name Type Description
hits CSV A table of motif matches
frequencies Matrix A table of sequence rows and columns of motif match frequencies
bgOut MotifSet Background frequencies of the nucleotides. This set will contain one motif that represents a single loci with the average frequencies of the nucleotides.


Name Type Default Description
background string "" A comma separated list (A,C,G,T) of the nucleotide background frequencies. An empty string means that the frequencies are estimated from the input sequencies. Frequencies are given for the forward (1) strand and they are automatically converted to their complements (A:=T, C:=G, G:=C, T:=A) for the reverse (-1) strand.
dropExt boolean false Drop motif file extensions from the output reports
forwardPos boolean false Convert backward strand coordinates to forward strand coordinates. Start coordinate will represent the last nucleotide of the hit and the end coordinate will represent the first nucleotide of the alignment if the hit is found from the reverse strand. Strand infromation and the matching sequence is preserved regardless of this parameter.
gap string "" Add a gap into the motifs: location minimum_length maximum_length. For example '6 0 8'.
pseudo float 0.0 Pseudo count for the scoring function
relativeScore boolean false Defines score limit relative to the motif configuration. Say min and max are the smallest and the greatest scores possibly obtained. Actual limit is (max-min)*scoreLimit+min.
reverse boolean true This flag can be used to include reverse complements of each sequence
score float 1.0 Score limit

Test cases

Test case Parameters IN
case1 properties motifs sequence (missing) (missing) (missing) hits frequencies bgOut

score = 10,
dropExt = true,

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