Applied Bioinformatics Course

SMART search

• Search SMART to find conserved domain for the post-floral-specific protein 1 (PPF-1, Swiss-Prot Accession: Q9FY06).
• Search SMART to find conserved domain for the RNA binding protein AT1G60000
• Search SMART to find conserved domain for the transcription factor SBP protein (At1g27370).

MEME search

• Search MEME to find conserved domain for the protein sequence of 15 Arabidopsis SBP transcription factors [15atsbp.fasta].

HMM search

• Use HMMER hmmbuild to build HMM model (atsbpd.hmm) for 15 SBP DNA binding domains (15atsbpd.fasta)
• Use HMMER hmmcalibrate to adjust the above HMM model (atsbpd.hmm).
• Use HMMER hmmsearch using the HMM model (atsbpd.hmm) to identify SBP DNA binding domains against maize transcription factors using the above HMM model.
• Build HMM model for 15 SBP DNA binding domains (15atsbpd.fasta).

Sequence logo

• Create a sequence logo for the SNPs of 20 SARS coronaviruses [20sars.fasta].
• Create a sequence logo for the the DNA binding domain of 15 Arabidopsis SBP proteins [15atsbpd.fasta].