This web page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison.

DNA motifs

MEME (Multiple Em for Motif Elicitation) is a motif-detecting software programs which can detect short, recurring DNA patterns that might have biological fucntions. There motifs usually indicate sequence specific binding sites for proteins that are involve in biological processes in the RNA level (ribose binding, mRNA splicing, transcription). The truncated FASTA-formatted KRAS DNA was used to detect the DNA motifs in the gene in the MEME program.

3 Motifs were found using MEME.

Motif 1

Motif 2

Motif 3

In addition, the FASTA-formatted KRAS DNA was analzyed by MOTIF, a motif-detecting software.

13 motifs were found using MOTIF with the following descriptions

1. EGF-like domain signature 1.
2. Insulin-like growth factor binding proteins signature.
3. Integrins beta chain cysteine-rich domain signature.
4. C-terminal cystine knot signature.
5. Anaphylatoxin domain signature.
6. 4Fe-4S ferredoxins, iron-sulfur binding region signature
7. Agouti domain signature.
8. Thiolases active site.
9. Tubulin subunits alpha, beta, and gamma signature.
10. Fungal hydrophobins signature.
11. VWFC domain signature.
12. 2Fe-2S ferredoxins, iron-sulfur binding region signature
13. Mammalian defensins signature.

Reference

1) Meme
http://meme.nbcr.net/meme4_3_0/intro.html
2) MOTIF
http://motif.genome.jp/