Bacteriophage sequence and evolution.

A collaboration between the laboratories of

Stephen C. Hardies and Philip Serwer.

with thanks to the Kleberg Foundataion and the Texas Coordinating Board.

Other resources.

Phage survey - under construction.

Using new isolation procedures developed by Dr. Serwer, to isolate phage species normally excluded by standard plating procedures.

To survey the abundance and diversity of phage species in different microecological segments of the bioshpere.

Environmental bacteriophage page

See Serwer P, Hayes SJ, Zaman S, Lieman K, Rolando M, and Hardies SC. 2004. Improved isolation of undersampled bacteriophages: finding of distant terminase genes. Vir. 329: 412–424.

Surveyed phages:

201phi2-1

201phi2-2.

702phi1-1.

G phage

Random primed PCR sample |

Subcloned sample & Q values |
Multiblastx vs. Swissprot.
Multiblastx vs. "tailed phages"[orgn].
Multiblastx vs. bacillus.

5 kb clone.

Comparative phage genomics. - Under construction

Goals:

To develop strategies for phage gene identification that go beyond a basic Psi-Blast search.

To tabulate data and methodology for use in subsequent phage genomes.

Psi-blast in restricted databases.
Proximity.
Prophages.
Undocumented genes.
Gene family building.

Procedural information. (10/9/03 and under construction)

Large terminase superfamily. (10/9/03 and under construction)

T7 extended superfamily (11/11/3).

Phage-host relationships.

RNA polymerase.

Families built on sfi21 genes.

Families built on bacteriophage lambda genes.

Families built on SPP1 genes.

Family database.

Software

Cut3.pl - a perl script that divides phd files at internal restriction sites, and marks vector junctions.
jAluI.dat - a sample vector junction definition file.
Phage analysis scripts.
abisplit.pl - Splits ab1 files to segments. Is useful for long chromatograms if they are to be processed by the Mac versions of ABI Sequence Analysis Software, but should not be needed for Windows or Linux versions. It is done to circumvent a bug in the Mac version that causes an integer overflow on long chromatograms.
Instructions for sending data to phredPhrap.

Student Outreach

Stephen C. Hardies.

.Home page (http://biochem.uthscsa.edu/~hs_lab).
e-mail: hardies@uthscsa.edu.

Philip Serwer.

Environmental bacteriophage page: (http://instinct.uthsca.edu/~serwer).
e-mail: serwer@uthscsa.edu.

at:

Department of Biochemistry.
The University of Texas Health Science Center at San Antonio.
MSC 7706.
7703 Floyd Curl Dr.
San Antonio, TX 78229-3900.