Difference between revisions of "BZIP study"

From Crop Genomics Lab.
Jump to: navigation, search
Line 21: Line 21:
 
=== Downloading and generating HMM consensus sequence file ===
 
=== Downloading and generating HMM consensus sequence file ===
  
# Download Stockholm alignment file from Pfam bZIP_1 > Alignment > Download options > Seed
+
# Download Stockholm alignment file from Pfam bZIP_1 > Alignment > Download options > Seed<p>Seed: the curated alignment from which the HMM for the family is built</p>
Seed: the curated alignment from which the HMM for the family is built
+
 
# 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 05:14, 20 April 2019

Contents

Identification

Pfam-based approach

HMM domain clans

Regarded as the main domain for bZIP transcription factor. Clearly distinguishes basic region and leucine zipper.

Used for further analysis.

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

  1. 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

  2. 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.