All of the information in the books Human Papillomaviruses 1995 and Human Papillomaviruses 1994, as well as numerous data files, are available to the public here on our World Wide Web site. We present here a guided tour of our site to familiarize new users with its various resources and capabilities. What you see on your screen now is one long document meant to be read in a distinctly old fashioned way from top to bottom, with nary a link to anywhere else in the world. Of course you can always escape from this linear tour by pressing the "Back" button on your browser.
If you are reading this page then you must know about Web Browsers and how to
move about the WWW. If you arrived at this site via a link from another site,
you may want to note our URL for future use: http://hpv-web.lanl.gov.
This is the address of the home page of the HPV Database and it looks like the
image outlined with a thick green line below. These images are copies of actual
pages or parts of pages on our Web site, but because they are merely graphics, the
links you see on them cannot be activated by clicking on them. In some of the
images you will see an icon of a hand pointing at a link.
Activating this link on our Web site would take you to the area displayed in the next
green-outlined graphic.
There are two branches to our site: (1) publications and (2) data. We will
follow the data branch first. As you scroll down through our home page you
come to an area labeled "II. Data" as shown here.
The data area of this Web site contains links to genetic sequences of papillomaviruses stored in GenBank, EMBL, and SWISS-PROT formats. It also contains links to alignments of papillomavirus genes and their proteins. These data files are stored on our ftp server. You can follow any of these links to that server and look there for any data you require. Another approach to finding the data you need would be to use the HPV Sequence Search mechanism, a link about to be opened by the pointing hand in the graphic above.
Upon clicking HPV Sequence Search the search area appears on the screen. An
explanation of how to use the search utility is included in the window. We type in a
search pattern -- in this example U12499, a GenBank accession number -- and hit the
carriage return.
The result of the search, an abbreviated GenBank file, appears. We
can retrieve the entire file by positioning the pointing hand on the link
called Sequence and clicking.
The result, the complete GenBank file, is shown as a cropped image in the
illustration below. This file may be transferred to your local computer in its
entirety by clicking on "File" in the menu bar at the top of the screen and
selecting "Save As . . ." from that menu. (Note! users of Netscape, for Macintosh, at
least, may have to use a slightly different procedure for downloading files. There
is a link entitled "Attention Macintosh Netscape users" on our home page. Consult
that for detailed instructions.) Our search mechanism is currently quite primitive.
You can only search for GenBank files. If you are interested in EMBL-format files you
will need to find them "by hand" on our ftp server.
If we return to the data area of the home page (II. Data) we can follow links to
alignment files.
This is what the alignments directory on our ftp server looks like. There is a folder
icon for each gene arrayed along the left edge of the page. There is also a fairly
complete ReadMe file that discusses the alignment files contained within the
folders. If we are interested in the E6 alignment we would open that folder as the
pointing hand is about to do.
Once inside the E6 folder we see there are two pairs of files. The files with
"formatted" in their names are the formatted nucleotide and protein alignments one
sees in printed publications; the other two files are the alignments in
"Intelligenetics" format.
The latter, unformatted files, are what you would want to download if you are
interested in manipulating the alignments or adding your own sequences to an
existing alignment. One such file, the HPV_E6.pro-aln amino acid
alignment is shown below.
This ends our introduction to the data resources of the Web site.
Let us now return to the HPV home page and follow the links that lead down the
other main branch of this site, the "on-line version of the
Human Papillomaviruses compendia." There are various routes we can
take to these publications. We can click the orange or green book covers at the top
of the home page or we can follow the links under part "I. The HPV Compendium,"
also on the home page.
Either way we arrive at the page displayed below. This page introduces the on-line
version of our publication and describes the Adobe Acrobat viewer which you will
need to view the publications. The viewer is free and can be obtained by following
the link shown below.
This is what the Adobe Acrobat page looks like. You can download the Acrobat
viewer appropriate to your computer (Mac, DOS, or UNIX) here.
Returning to the compendium introduction at our site (below) we can view the
tables of contents of the 1994 or 1995 Human Papillomaviruses
publication either by clicking on the links in the first line, or scrolling down the
page to where the Tables of Contents begin.
The graphic below shows a part of the
table of contents of the 1995 book. The pointing hand is about to retrieve an
article on mRNA transcript maps from Part III. This link, though it looks the same as
others, behaves differently. A copy of the mRNA transcript file is transferred to
your local computer and the Adobe Acrobat viewer is automatically launched. Acrobat
is a "helper application" used to read files that are in a format which is
nonstandard for the WWW.
The Acrobat viewer displays the mRNA transcript article (see below), which is
written in "portable document format" (PDF), and allows you to print out a perfect
copy of it, exactly as it appears in the printed compendium. Acrobat viewer has a
search mechanism that allows you to search in a document for words that might lead
you to a subject of interest. For example, Part V of the compendium lists hundreds
of HPV references. Those references are searchable with Acrobat Viewer. Searches for
specific nucleotide sequences in Part I (e.g.
AATAAA) will be less useful because of the way GenBank files are formatted, with
spaces and sequence numbers embedded in the file.
Our Web site provides users an opportunity to communicate with us from several
points on the site. An electronic "comments" form can be activated
that allows you to write us a letter to which we promise to respond.
Finally, we
have connected our site to several other locations of great utility to biologists
as shown below. The link to these sites occurs at the bottom of the home page.
This is a real link back to our home page!