Identification of putative cis-regulatory elements in Cryptosporidium parvum by de novo pattern finding

doi:10.1186/1471-2164-8-13

BMC Genomics
Volume 8

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Abrahamsen MS
Kissinger JC

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Research article

Identification of putative cis-regulatory elements in Cryptosporidium parvum by de novo pattern finding

Nandita Mullapudi¹ , Cheryl A Lancto² , Mitchell S Abrahamsen² and Jessica C Kissinger¹

¹Department of Genetics & Center for Tropical and Emerging Global Diseases, Paul D. Coverdell Center, D.W. Brooks Dr., University of Georgia, Athens, GA 30602, USA

²Veterinary and Biomedical Sciences, University of Minnesota, St Paul, MN 55108, USA

author email corresponding author email

BMC Genomics 2007, 8:13doi:10.1186/1471-2164-8-13


Published:	9 January 2007

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Additional File 2:

Top ten motifs reported by each algorithm. Top scoring motifs found by both MEME and AlignACE and their respective E-values and scores. Candidate motifs reported in Figure 2 and 3 are denoted in bold. Note that the motifs found by the two programs are never identical. We used positional information to deduce overlapping motifs, and used the motifs identified by AlignACE to represent the consensus since AlignACE found more than one occurrence of the same motif within the same sequence and hence produced a more degenerate motif.

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Additional File 3:

Information content and occurrences of candidate motifs reported in the paper. This table describes the Information content values as determined by MEME for each of the candidate motifs reported in the paper. Additionally, the occurrences of these motifs within their respective sub-set and the global occurrence within the whole genome (in intergenic regions) is reported.

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Additional File 1:

Primer sequences for comparative PCR experiments. Oligonucleotide primers used in this study. L= left or forward primer; R= right or reverse primer.

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