- Find protein sequences of all Arabidopsis squmosa promoter binding transcription factors (SBP) from the database of Arabidopsis transcription factors (DATF).
- Make sequence alignment of SPL3 and SPL4. Find exons from these two SBP TFs using the GSDS online web server.
- Make phylogenetic analysis for Arabidopsis 15 SBP DNA binding domains (15atsbpd.fasta)
- Find functional domains of SPL1 and SPL3 using SMART.
- Find conserved domains for among 15 Arabidopsis SBP TFs [atsbp15.fasta].
- Build HMM model for 15 SBP DNA binding domains (15atsbpd.fasta).
- Search SBP DNA binding domains against maize transcription factors using the above HMM model.
- Compare the above BLAST and HMM search results.
- Find all putative SBP genes via BLAST search against all online genome and EST databases.
Refrences
- Riese M, Höhmann S, Saedler H, Münster T, Huijser P. Comparative
analysis of the SBP-box gene families in P. patens and seed plants. Gene.
2007 Jul 10;
[Abstract] - Yang Z, Wang X, Gu S, Hu Z, Xu H, Xu C. Comparative study of SBP-box
gene family in Arabidopsis and rice. Gene.
[Abstarct] - Cardon G, Höhmann S, Klein J, Nettesheim K, Saedler H, Huijser
P. Molecular characterisation of the Arabidopsis SBP-box genes. Gene.
1999 Sep 3;237(1):91-104.
[Abstract] - Guo AY, Zhu QH, Gu XC, Ge S, Yan J and Luo JC. Genome-wide identification
and evolutionary analysis of the plant specific SBP-box transcription
factor family.
[Abstract] - Luo JC, Analysis of Arabidopsis SBP gene family (in Chinese0.
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