Prime User Manual - ISP

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20 Chapter 3: Prime–Structure Prediction: Initial Steps Prime 2.1 User Manual Figure 3.3. The Find Homologs step, initial view. 3.2.2 Searching for Homologs To launch a search for homologs: • Click Search (near the middle of the panel). Depending on what is selected in the Find Homologs–Options dialog box, BLAST or PSI- BLAST is used to search for templates. The default is to use BLAST to search the nonredundant PDB database that has been loaded with Prime. For search options, see Section 3.2.3.
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. Prime 2.1 User Manual 21
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Page 3 and 4: Contents Document Conventions .....
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Alignment Section Chapter 8: Maestr
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Files Chapter 11: Command Syntax In
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Prime User Manual Chapter 12: Comma
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Table 12.1. Keywords for the seqcon
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Chapter 12: Command-Line Utilities
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Prime User Manual Appendix A: Third
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Prime User Manual Appendix B: Envir
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Prime User Manual Appendix C: File
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Prime User Manual Appendix D: Error
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!UNUSABLE: SEQRES numbering is wron
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Prime User Manual Getting Help Schr
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Getting Help If Maestro fails, an e
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Prime User Manual Glossary Chapter
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Symbols + (plus sign), in Pfam sequ
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K killing jobs ....................
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sequences coloring.................
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