HorA Sever Tutorial

Database Search

Database search mode compares the query protein (your protein of interest) to proteins in SCOP database (40% identity representatives), and you will get an email containing the link to the result page like the one shown above.

The result is a table of proteins that are likely homologous to the query protein. More probable homologs appear on the top and less probable homologs appear at the bottom. The SVM score is a predictive score from the model built to find homologous proteins combining many different sequence similarity scores and structural similarity scores (details in reference). The probability conveniently measures how probable the hit protein (from database) is homologous to the query protein. The rest of the columns are information about the hit protein. SCOPid is the hit protein’s (or domain’s) unique identifier in SCOP database. Protein, SCOP family, SCOP superfamily, SCOP fold, and SCOP class show the classification of the hit protein in the SCOP database.

Pairwise Comparison

Pairwise comparison mode compares two proteins submitted, and you will get an email containing the link to the result page like shown above.

The result shows similarity scores between the two proteins of interest and the alignments between them. The SVM score is predictive score from the model built to find homologous proteins combining many different sequence similarity scores and structural similarity scores (details in reference). The probability measures how probable the two proteins of interest are homologous. DALI Z-score is Z-score from DALI structural comparison program developed by Holm group. HHsearch score is probability from HHsearch HMM comparison program developed by Soding group.