Prime User Manual - ISP

To identify a family for the query (optional):
• Click Find Family to run HMMER/Pfam.
Chapter 3: Prime–Structure Prediction: Initial Steps
This helps identify the family that best matches the query sequence. This job should take
only a few minutes.
The query family name found appears in the Query family name text box with an E-value in
parentheses. If the E-value of the family is too large, it is not meaningful to consider the family.
The sequence viewer shows the match between the query and the consensus sequence of the
family. If this sequence, labeled NAME_pfam, is not visible, check for a plus sign to the left of
the query name: +NAME. Click the plus sign to show any hidden sequences. The match
sequence displays information about which residues are conserved in the multiple sequence
alignment used to generate the Hidden Markov Model (HMM). Capital letters indicate highly
conserved residues, lowercase letters indicate a match to the HMM, + means the match is
conservative, and a blank indicates that the residue does not match the HMM.
3.2.3 Find Homologs Search Options
To change search options:
• Click Options to open the Find Homologs–Options dialog box.
You can use this dialog box to specify a PSI-BLAST or BLAST search, or change the settings
for either type of search.
General options include:
• Database
• Similarity Matrix
• Gap Costs
• Expectation value
• Word size
• Filter query (off by default)
PSI-Blast options include:
• Inclusion threshold
• Number of iterations
The default database selection is NCBI PDB (all). Other selections include:
• NCBI PDB (non-redundant)—Does not include PDB files with identical sequences.
• NCBI NR—Recommended for PSI-BLAST runs. With this selection, only the sequences
with structures available in the PDB are displayed in the Homologs table.
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