Solanaceae Ortholog and Paralog Database Search

Best Hits Method

PlantGDB-assembled Unique Transcript (PUT) assembly sets for 11 Solanaceae species were obtained from the PlantGDB PUT database. These sets were searched against each other using TBLASTX. A cut-off of 10^-5 was used to identify the best hits across Solanaceae species. Paralogs were required to be at least 45% identical over 225 bp.

To search the database, enter a PUT identifier and find matches within the same species (paralogs) or in other Solanaceae species (orthologs).

PUT identifiers are of the form PUT-version_tag-scientific_name-number, where version_tag is the PUT release number, scientific_name is the species name with spaces replaced with underscores, and number is an unique integer value assigned to each PUT. [see details at PlantGDB]

OrthoMCL Clustering Method

The Solanaceae PUT sequences were translated using ESTScan 2.1 and the resulting polypeptide sequences were clustered using OrthoMCL to produce clusters containing putative orthologs/in-paralogs.

Since each set of Solanaceae translated PUT sequences represents an incomplete proteome, the more complete proteomes of the model genomes Arabidopsis, Poplar, and Grape were included in the analysis to help resolve orthologous relationships in cases where true orthologs were absent from one or more of the Solanaceae translated PUT sequence databases.

Each cluster member sequence was compared to the UniProt UniRef50 database using BLASTP, and hits with an E-value <1e-5 were retained. Functional annotation text associated with the UniRef50 sequences was slightly processed to improve the clarity/information content of the text, and the resulting combined text from all cluster members is associated with each cluster to enable text searching.

The OrthoMCL cluster results can be searched by PUT identifier (see above), cluster identifier, or by cluster annotation keyword search.