PSAT User's Manual

8. Retrieving a list of homologs for a complete genome

In this part of the tutorial, you will create a list of all genes in F. tularensis subsp. tularensis SchuS4 and their homologs in other genomes.

1. Select Francisella_tularensis_tularensis as the Reference Genome.


2. Select a few other genomes as the Comparison Genomes.


3. Select the analysis method Get homolog list for a complete genome.


4. Leave the default BLAST alignment score thresholds setting to the default option (e-value<0.1, bit score > 200, % identity > 30%). The tool will look for BLAST hits that meet all of these cutoff values when determining what to consider a homolog in this analysis. The results can change dramatically when choosing different threshold scores.


5. Leave the display option set to the default value to show all hits for each comparison genome.


6. Leave the display option set to the default value to only show hits with a homolog clustering score of at least 2.


7. Select the Submit button to submit the form. The results will list all genes found in Francisella tularensis SchuS4 and their homologs (satisfying the specified constraints) in each selected comparison genome.




8. Select one of the rows in the results. This will take you to Genomic Neighborhoods page for this entry.
   
   
9. Go back to the input page and select the output format Tab delimited text file. Click Submit and you will see the same results in tab delimited format. From your browser menu, select File | Save As to save the file. Select Text File Format, and use the .xls extension in the filename if you would like to view results using MS Excel.