Contents

1. Introduction to Protein Analysis
2. Obtain a sequence of interest.
3. Identify ORF's and translate into protein
4. Identify Similar Proteins from the Databases
5. Align your sequence vs similar sequences and look for Gene Families
6. Determine the putative function of your protein
7. Determine the putative structure of your protein
8. Protein Structure Visualization Tools
9. Other Interesting Things You Can Do With Proteins

IV. Identify Similar Proteins from the Databases

1. Search against plain sequence databases
   
   1. Search the databases (GenBank, etc.) using BLAST 2.0 from NCBI
      Other variations of the basic BLAST program are available from NCBI. They are listed below. They all use the same basic parameters that we have already discussed for BLAST 2.0.
      
   2. PSI-BLAST (Position-Specific Iterated BLAST)
      long & horrible URL
      Example
      
      • Used for detecting weak similarities between protein sequences
        
      • Program first does a gapped BLAST
        
      • Information from the resulting hits is used to build a position specific scoring matrix
        
      • The scoring matrix is used instead of the query for the next round of searching
        
      • PSI-BLAST may be iterated until no new significant hits are returned
        
   3. PHI-BLAST (Pattern Hit Initiated BLAST)
      same form as above
      
      • Input is protein sequence and a motif that is found in that sequence
        
      • Input patterns must be in Pro-Site format
        
      • Statistical significance is still reported as an E value, but the calculation method is different
        
      • PHI-BLAST is integrated with PSI-BLAST therefore results can be used to initiate a second round of searching
        
2. Search against species-specific sequence databases
   
   1. Advanced BLAST
      
      • 22 species available
        
      • Copy and paste your protein or DNA sequence of interest
        
      • Choose from the available organism menu.
        
      • submit the sequence for analysis
        
   2. Organism Specific Databases
      http://restools.sdsc.edu/biotools/biotools10.html
      
      1. One of the most complete listings available of all the various organism specific database projects around the world
         
3. Search against the PDB database
   
   1. PDB's FASTA interface
      http://www.rcsb.org/pdb/cgi/queryForm.cgi?PDBId=1&TypeSelection=1&ExperimentalTechnique=1&Fasta=1
   2. Advanced BLAST
      
   3. GenQuest Q Server
      http://www.bis.med.jhmi.edu/Dan/gq/gq.form_rm.html
      • Perform BLAST, FASTA, Smith-Waterman against
        
      • PDB - Protein Databank sequences of proteins with solved structures
        
      • Swissprot - a protein sequence database
        
      • Prosite - a library of protein motifs
        
      • The Genome Sequence Database (GSDB)