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2016 ; 12
(ä): 26
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ExactSearch: a web-based plant motif search tool
#MMPMID27134638
Gunasekara C
; Subramanian A
; Avvari JV
; Li B
; Chen S
; Wei H
Plant Methods
2016[]; 12
(ä): 26
PMID27134638
show ga
BACKGROUND: Plant biologists frequently need to examine if a sequence motif bound
by a specific transcription or translation factor is present in the proximal
promoters or 3' untranslated regions (3' UTR) of a set of plant genes of
interest. To achieve such a task, plant biologists have to not only identify an
appropriate algorithm for motif searching, but also manipulate the large volume
of sequence data, making it burdensome to carry out or fulfill. RESULT: In this
study, we developed a web portal that enables plant molecular biologists to
search for DNA motifs especially degenerate ones in custom sequences or the
flanking regions of all genes in the 50 plant species whose genomes have been
sequenced. A web tool like this is demanded to meet a variety of needs of plant
biologists for identifying the potential gene regulatory relationships. We
implemented a suffix tree algorithm to accelerate the searching process of a
group of motifs in a multitude of target genes. The motifs to be searched can be
in the degenerate bases in addition to adenine (A), cytosine (C), guanine (G),
and thymine (T). The target sequences to be searched can be custom sequences or
the selected proximal gene sequences from any one of the 50 sequenced plant
species. The web portal also contains the functionality to facilitate the search
of motifs that are represented by position probability matrix in above-mentioned
species. Currently, the algorithm can accomplish an exhaust search of 100 motifs
in 35,000 target sequences of 2 kb long in 4.2 min. However, the runtime may
change in the future depending on the space availability, number of running jobs,
network traffic, data loading, and output packing and delivery through electronic
mailing. CONCLUSION: A web portal was developed to facilitate searching of motifs
presents in custom sequences or the proximal promoters or 3' UTR of 50 plant
species with the sequenced genomes. This web tool is accessible by using this
URL: http://sys.bio.mtu.edu/motif/index.php.
free
free
free
