| this color |
| this color |
| R/G | S4 | C58 | K84 | R. etli | R. leguminosarum | S. meliloti | M. loti MAFF | M. loti BNC |
| 1 | 2nd chromosome | linear chromosome | 2nd chromosome | - | - | - | - | - |
| 2 | plasmid 630kb | AT plasmid | plasmid 390kb | plasmid F 640kb | plasmid pRL12 870kb | plasmid pSymA | plasmid 1 | plasmid 1 |
| 3 | plasmid 259kb | Ti plasmid | plasmid 179kb | plasmid E 510kb | plasmid pRL11 680kb | plasmid pSymB | plasmid 2 | plasmid 2 |
| 4 | plasmid 210kb | - | plasmid 44kb | plasmid D 370kb | plasmid pRL10 490kb | - | - | plasmid 3 |
| 5 | plasmid 130kb | - | - | plasmid C 250kb | plasmid pRL9 350kb | - | - | - |
| 6 | plasmid 79kb | - | - | plasmid A 190kb | plasmid pRL7 150kb | - | - | - |
| 7 | - | - | - | plasmid B 180kb | plasmid pRL8 150kb | - | - | - |
What you see in these tables is an alignment of orthologs computed across 11 different genomes. Each column is a genome; each row is an ortholog family; in each cell you see a gene identifier (using genBank GI numbers in most cases). The product description at the right hand side is taken from the genome that anchors the table. Each table is sorted by one of the genomes (the anchor). The C58 table is sorted by the C58 genes; The S4 table by the S4 genes; and so on. Ortholog families in which genes from the anchor genome do not participate are not represented in the table.
The colors of cells are according to the table above. In general the same color was assigned to related replicons, but there are replicons colored the same that are not related; don't be fooled! If a cell is empty (except for the genome identifier) this means that that genome does not participate in that ortholog family.
The primary input for all Ortholog Alignments was the sets of orthologs computed by OrthoMCL, a program developed at David Roos's lab at UPenn, based on the TribeMCL program developed by C. Ouzonis and others. These ortholog families are fairly reliable (but not error-free).
Paralogs (ie if an ortholog family contains more than one gene from the same genome, those genes are being defined here as paralogs) are represented as mini-tables inside cells. Note that for the anchor genome this is what happens: if genes g, h, and k are paralogs, the rows for g, h, and k are the same.
Synteny was not used to construct these tables; instead, these tables can be used to locate syntenic blocks. This is possible because the locus tags used to index cells are for the most part sequential (in a physical genome sense). In other words, if you see numbers down a column (not the sorted [or anchor] column!) that are consecutive or nearly so, this means this is a syntenic block. Exceptions to this sequential numbering are few (example: virB7 in S4 is not in order).
Last updated by Joao C. Setubal, September 1st, 2008.