Downloading the T. pallidum sequence in FASTA and GCG format by ftp from the University of Texas-Houston (UTH)


Revised 17 July, 1998

GCG programs require that the sequence files contain no more than 325,000 nt. The file containing the T. pallidum sequence in the Fasta format (gtp4.1.seq) is a single contig of 1,138,011 nt. Coordinates and annotations in later versions may change as the result of additional corrections.

To make it easier to create a GCG database from the T. pallidum sequence, the contig has been subdivided into four GCG-formatted sequence files:

gtp4.1a.seq		nt 1-300,000
gtp4.1b.seq		nt 300,001-600,000
gtp4.1c.seq		nt 600,001-900,000
gtp4.1d.seq		nt 900,001-1,138,011

Instructions for downloading these four sequence files are provided below.

Use a user-friendly ftp interface to download the four files listed above, or alternatively enter the following commands from a unix prompt:

ftp utmmg.med.uth.tmc.edu
Login: anonymous
Password: type in your email address here
ftp> cd pub
ftp> cd t_pallidum
ftp> bin (this sets the ftp mode to binary)
ftp> mget *
(Answer y to each prompt.)
ftp> quit

At any point, you may use the pwd and dir commands to see where you are and what files are there.

Questions, requests, or comments: treponema@utmmg.med.uth.tmc.edu

T. pallidum home page