MBGD/Profile search

MBGD

Profile search (phenotype)†

1. Click "Phenotype" tab.
2. Select phenotype in "List of phenotype"
3. The genus will be selected.
4. Using ">>>" you can add selected genus to the "Presence organisms" or "Abesence organisms"
5. Click “Analyze” to run a profile search.

Profile search (environment)†

1. Click "Environment" tab.
2. Select phenotype in "List of environment"
3. The genus will be selected.
4. Using ">>>" you can add selected genus to the "Presence organisms" or "Abesence organisms"
5. Click “Analyze” to run a profile search.

Profile search (taxonomy)†

1. Click "Tax" tab.
2. Select phenotype in "List of taxonomy"
3. The genus will be selected.
4. Using ">>>" you can add selected genus to the "Presence organisms" or "Abesence organisms"
5. Click “Analyze” to run a profile search.

Profile search (MBGD ortholog cluster)†

1. Click "MBGD ortholog cluster" tab.
2. Enter cluster id in MBGD ortholog cluster id.
3. The genus will be selected.
4. Using ">>>" you can add selected genus to the "Presence organisms" or "Abesence organisms"
5. Click “Analyze” to run a profile search.

Profile search (File)†

1. Click "File" tab.
2. Create file according to format

    The file format should be comma-separated data and correspond to the following format:
    
      Column 1: Species name, genus name, taxonomy ID
      Column 2: Numerical value (1/0), string (A/B/O), numerical value (with freely set thresholds)
          Ultimately, the values will be evaluated as numbers, with 1 = presence and 0 = absence.
          If strings are used, conversion rules to numbers are required. Example: A/B = 1, C = 0.
          If thresholds are to be applied to numerical values, use the following format:
          # 0.5 and above to 1  
          # 0.2 or less to 0  
          # between 0.3 and 0.5 to 1  
    Items that belong to neither (neither presence nor absence) should be left empty.
3. Upload your file.
4. Click “Analyze” to run a profile search.

Overview of MBGD

Introduction

• Overview
• Functions
• References

Quick Tour

• Select & View ortholog table
• Searching ortholog data
• Create ortholog table

MyMBGD

• Login/Create User
• MyMBGD top page
• Import Genome Data
• Genome Annotation by Ortholog Group Assignment
• Ortholog Clustering
• Result Manager
• Genomaple