Derivation of phageDseq6-9-4 files: This link describes trimming of an artifical terminal repeat and a chimeric sequence read to convert the raw consed contig listing to the first circular sequence.  The phageDseq6-9-4 files themselves and some preliminary analysis listed in this link are now obsolete due to some edits (deletion of two bases) during proofing, but the logic of the trimming is still the same.

phageDseq6-17-4 files:  These were derived as above, but from the consed output after deletion of two bases.

• Characteristics:
• Length:  156,938 base pairs.
• Ends (direct orientation): CTCCAAGGCTTCTAGAACCTCGTTAG...AAAGCACCTCATAAATAAAGAAGTCACT
• Orientation: has the terminase on the direct strand.
• End point in circle is arbitrary, and suspected physical terminal repeat is not yet represented.
• Nucleotide sequence files:
• Direct
• fasta (phageDseq6-17-4.fasta)
• GCG (phageDseq6-17-4.seq)
• Complement
• fasta (phageDseq6-17-4c.fasta)
• GCG (phageDseq6-17-4c.seq)
• GeneMark predictions (in phageDseq6-17-4 coordinates).
• Collation of GeneMark predicted frames
• Details of the GeneMark predictions.
• Index of information about open reading frames (obsolete; see feature viewer below).
• Through cursory examination of Psi-Blast results, and rpsblast results.
• Mysql orf data viewer. (obsolete; data viewed is frozen at an early point, see feature viewer below for current view of data.).
• Restriction digestions and exploration of the ends.
• In summary: on circular sequence phageDseq6-17-4, there is a 6941 bp terminal redundancy mapping at positions (130,446 - 178)..(137,386 - 178).

phageDseq7-20-4 sequences:

• Sequence files:
• One base removed due to final conservation, and sequence rearraged to account for identification of terminal direct repeats.  Derivation of phageDseq7-20-4.
• 163,878 bp, GGGTAGAGAGGGGGCTAGGGTA...GCATCCGATTTACACGCCC
• 6941 bp terminal direct repeats (1..6941) and (156938..163878).
• fasta direct (terminase on + strand) (phageDseq7-20-4.fasta)
• GCG direct (phageDseq7-20-4.seq)
• fasta complement (phageDseq7-20-4c.fasta)
• GCG complement (phageDseq7-20-4c.seq)
• Segments:
• 1..100,000 (pD7-20-4_1-100k.fasta)
• 100,001..end (pD7-20-4_100001-163878.fasta)
• tRNA predictions. (two predicted).
• Promoter predictions.
• Mysql feature viewer.
• Summary of coiled coil findings.
• Gbrowse for phageD.
• Index of new blast hits, 12/8/4.
• Index of new psiblast hits 8/26/5.
• Index of new psiblast hits 7-20-6.
• Summary of hmmer results. (7-21-6)
• All that is known re PhageD structural proteins
• Mass spec data - list of Mascot jobs completed in 2005
  
• Mass spec data (2006)
  

Staphylococcal phage K for comparison

• Mysql feature viewer.
• Gbrowse for Staphyloccocal phageK.
• StaphK fasta file.
• promoter predictions.

Lactobacillus plantarum phage LP65 for comparison

• Summary information.

Obsolete entries:  Some notes made early during sequencing that may yet be worth retrieving.