CyanoCOG: A database of cyanobacterial orthologous proteins

The CyanoCOG identified cyanobacterial orthologous proteins on the basis of orthologous concept, which based on all-against-all sequence comparison. This database allows the user to search and analyzed various clusters of protein from many cyanobacterial genomes.

User can be find proteins or cluster of your interest through the following main features:

  1. Search protein by keywords
  2. Find phyletic pattern (keyword filters)
  3. Search protein by sequence
  4. View multiple sequence alignment (msa) in an ortholog

1. Search protein by keywords [top]

Use a keyword or words, which describes the target protein and must be in alphanumeric characters such as 'chlorophyll a synthase' or 'SPLC1_S530330'. Also, multiple keywords can be search by putting commas (,) between words for word-exactly matches; optionally, semicolons (;) for word-containing match. On the search page, user can select the desire organisms using the option on organism list. When user click the "search" button, many clusters that match to the keyword will be displayed on the search results.

Likewise, if the user will be focus the cluster of orthologous proteins based on their functional relationship, user can input target category in the box of "Functional Category" or select from category list that based on NCBI-COGs and Cyanobase classification.

Search protein by keywords

Search Results: Many search results in the term of cluster of orthologous proteins are listed. In each row, there are divided into six cells: (1) ortholog ID, (2) gene information, (3) gene symbol, (4) gene description (descriptive function of the gene) (5) functional category and (6) note.

If user clicks on the 'OrthologID', the gene members in this cluster will be displayed. If user clicks on the 'Gene Info', the descriptive data of selected gene/protein will be displayed (direct linked to NCBI protein page).

Search Results

When the user clicks on the 'Protein domains' box that placed on the right hand, domain prediction for each protein will be showed.

Show protein domains

2. Find phyletic pattern (keyword filters)[top]

If user wants to search or analyze pattern of orthologous proteins in the group of cyanobacteria. The pattern page provides two methods to select clusters of orthologous proteins include of 'keyword' and 'functional category' searches. When user clicks 'Search' button, the pattern results will be displayed.

Find phyletic pattern

Phyletic Pattern results: In the phyletic pattern results, target proteins of interesting organisms are displayed in the matrix. Indexing in matrix is done using two entries - ortholog ID for the rows and organism names for the columns. In the matrix, 'value' in each cell represents number of proteins that are members within the cluster. If user clicks on the 'Ortholog ID', the gene members in this cluster will be displayed.

Phyletic pattern results

3. Search protein by sequence[top]

If user has a protein or DNA sequence, you can be getting clusters of orthologous proteins by using the BLAST page to perform the BLAST search. Then, the BLAST search is done against the database. List of homologs will be displayed as the format of NCBI's BLAST page.

BLAST programs, databases and parameters can be adjusted that depend on the user's objective.

Search protein by sequence (BLAST search)

BLAST Results

4. View multiple sequence alignment (msa) in an ortholog[top]

If user chooses to select all cluster of orthologous proteins, you can click 'search' button without specify keyword and function category. In the result matrix, user can be set selection for individual organisms or organism groups of your interest through two methods. First, user can select or unselect the individual organisms by using the add/remove organisms listed in the panel (on left-hand side). Alternatively, user can use the checkboxes in the header (on right-hand side) to indicate that your search should be restricted to include only organism groups (such as 'unicellular', 'filamentous' or 'extreme environment') with the checked terms.

View multiple sequence alignment (msa) in an ortholog

In the pattern result page, a separate section helps to provide additional information about sequence regions containing the same, or similar, pattern of amino acids in each cluster of orthologous proteins that showing in the multiple sequence alignment page. User can click on the text under the 'orthoID' to open the multiple sequence alignment pages.

Summary view of msa

Multiple sequence alignment view