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SyMAP convert |
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| Genome | NCBI* | Ensembl | ~Length |
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| Arabidopsis thaliana | Chr 1-5 | Chr 1-5 | 119M |
| Oryza Sativa (rice) | Chr 1-12 | Chr 1-12 | 373M |
| Solanum tuberosum (potato) | Scafs 14,852 | Chr 0-12 | 800M |
| Solanum lycopersicum (tomato) | Chr 1-12 | Chr 1-12 | 807M |
| Caenorhabditis elegans | Chr I,II,III,IV,X | Chr I,II,III,IV,X | 100M |
| Sus scrofa (pig) | Chr 1-18, X, Y | Chr 1-18, X, Y | 2,435M |
| Danio rerio (zebrafish) | Chr 1-25 | Chr 1-25 | 1,345M |
| Bemisia tabaci (whitefly) | Scafs 19,750 | Scafs 227 | 615M |
These were all converted and loaded into SyMAP, but only the smaller ones were analyzed for synteny.
There may be variations that I did not account for, hence, you may want to edit the script to tailor it. Alternatively, you can contact me (symap@agcol.arizona.edu) and I will make the edit for you.
The two scripts are very similar except some of their keywords and naming conventions vary. Also, ConvertNCBI detects different products of the mRNAs for the same gene, and condenses them to one. It also allows hard-masking of a soft-masked genome sequence, which is not necessary for Ensembl since it offers both types of files.