Abstract
Background
The position and orientation of cis-elements plays key role in the process of transcription. Binding sites of the transcription factor is very specific and confined within array of nucleotides on promoter sequence of a gene. Also, presence of a binding site influences the action of other cis-elements present in the vicinity. Such positionally conserved motifs with particular distance (in units of a base) between them could be responsible for the similar kind of function.
The position and orientation of cis-elements plays key role in the process of transcription. Binding sites of the transcription factor is very specific and confined within array of nucleotides on promoter sequence of a gene. Also, presence of a binding site influences the action of other cis-elements present in the vicinity. Such positionally conserved motifs with particular distance (in units of a base) between them could be responsible for the similar kind of function.
Result
To detect positionally conserved motifs, we have developed a novel motif detection program 'MotDet'. It allows user to search given motif(s) in confined range of positions and also allows combinatorial search of two motifs present at peculiar distance across the given source sequence(s). Such analysis is not feasible with the available tools.
To detect positionally conserved motifs, we have developed a novel motif detection program 'MotDet'. It allows user to search given motif(s) in confined range of positions and also allows combinatorial search of two motifs present at peculiar distance across the given source sequence(s). Such analysis is not feasible with the available tools.
Conclusion
Using MotDet, one can detect a motifs with conserved position across the given source sequences which could be responsible for crucial biological process. Using software one can also detect the co-occurring motifs with peculiar distance across the submitted source sequences and hence could hypothesize co-regulation of the genes.
Using MotDet, one can detect a motifs with conserved position across the given source sequences which could be responsible for crucial biological process. Using software one can also detect the co-occurring motifs with peculiar distance across the submitted source sequences and hence could hypothesize co-regulation of the genes.
Funding: This work was supported by the Department of Information Technology, Government of India [Grant numbers: DIT/ (R&D)/BIO/15(9)/2006 to A.K.K, DIT/R&D/BIO/15(5)/2008 to A.K.K]