Difference between revisions of "BZIP study"
From Crop Genomics Lab.
KangHeum Cho (Talk | contribs) |
KangHeum Cho (Talk | contribs) |
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Seed: the curated alignment from which the HMM for the family is built | Seed: the curated alignment from which the HMM for the family is built | ||
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# Use '[http://www.ibi.vu.nl/programs/prcwww/hmmbuild.html hmmbuild]' command from HMMER software to convert Stockholm alignment into a profile HMM | # Use '[http://www.ibi.vu.nl/programs/prcwww/hmmbuild.html hmmbuild]' command from HMMER software to convert Stockholm alignment into a profile HMM | ||
Revision as of 05:12, 20 April 2019
Contents |
Identification
Pfam-based approach
HMM domain clans
- bZIP_1 (PF00170)
Regarded as the main domain for bZIP transcription factor. Clearly distinguishes basic region and leucine zipper.
Used for further analysis.
- bZIP_2 (PF07716)
Conserved basic region, weaker leucine zipper.
- bZIP_Maf (PF03131)
No distinct basic region. No clear leucine zipper interface.
Downloading and generating HMM consensus sequence file
- Download Stockholm alignment file from Pfam bZIP_1 > Alignment > Download options > Seed
Seed: the curated alignment from which the HMM for the family is built
- Use 'hmmbuild' command from HMMER software to convert Stockholm alignment into a profile HMM
hmmbuild [options] hmmfile alignfile
hmmbuild reads a multiple sequence alignment file alignfile , builds a new profile HMM, and saves the HMM in hmmfile.