Sequence analysis of environmental phage isolates.

Stephen C. Hardies, Mandy Rolando, Chris Kawasaki, Borries Demeler, and Philip Serwer.

Concept of the phage sequence survey:

• phageD sequence survey.  Commentary.
• phage D restriction data.   Commentary.

• GBrowse of phiNIT1 region. Commentary.
• 6942 bp terminal repeats.      Commentary.
 
• GBrowse detailed display of left terminal repeat of phageD.
• early promoters.
• Screen shot of full phageD GBrowse with promoters, regions, CC displayed.
• GBrowse display of StaphK. Commentary

• Large Terminase superfamily.
 
• VpV secondary structure figure. - positional strategy and the secondary structure strategy.  Commentary.
• terminase_tree.  Commentary
• Judging the alignment by secondary structure prediction. Commentary
• With psipred predicting over the full non redundant database.
• With psipred prediction confined to the family members.
• With the psipred neural net applied directly to the SAM alignment directly.
• What is learned about large terminase?
• P-loop domain.   commentary
• GBrowse display.
• P-loop model.
• C terminal domains -  commentary
• GBrowse display.
• Myoviral baseplate wedge.html.- commentary

• RNA polymerase tree.  - commentary
• Portal protein - commentary.
• Tail sheath protein.
• phage N vs. phageD survey. commentary.

• Automatically computed indel chain across phageD vs. StaphK.   - commentary.
• Automatically computed indel chain around large terminase.