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Web resources of chlamydial interest
Please note:
www.chlamydiae.com
has no control of the changing content of sites to which it links. The existence
of a link from this site does not imply endorsement of that site. This page
being updated Jan 2008.
Chlamydial Genomics and proteomics
Stanford /
Berkely Chlamydia genomics project C. trachomatis D & L2; C. pneumoniae
CWL 029 [C. trachomatis serovar D was the first
chlamydial genomic sequence in a project shared between Berkeley (Richard
Stephen's group) and Stanford (Ron Davies group). The original Berkeley site has
disappeared and this site was last updated in 1999 and has been surpassed by
other genomics sites. However this was an historic collaboration, making high quality genomic data available to the
research community as it happened. Anybody who provides quality whole genome
sequence data for the very first time deserves 3 star rating]. Accessed 2/1/2008 
Chlamydia trachomatis serovar A. Sanger Institute 1.052Mb; C. trachomatis
Serovar B [Latest sequences.
Databases available but finishing still in progress, publication pending].
Accessed 2/1/2008
Chlamydia
trachomatis Jali (Gambia) Serovar B 1.04 Mb [Latest
sequences. Database available but finishing still in progress, publication
pending]. Accessed 2/1/2008
Chlamydia trachomatis serovar L2 1.038 MB [Latest
sequences. Database available but finishing and gene prediction still in
progress, publication pending] Accessed
2/1/2008
C. muridarum (Nigg strain)
Accessed 2/1/2008
Chlamydophila
abortus genome S26/3 Wellcome Trust Sanger Institute and Moredun
Institute.
Associated publication [961 predicted coding
sequences, 842 conserved in other Chlamydophila; no toxin genes; no genes for
tryptophan metabolism or nucleotide salvage]. Accessed 2/1/2008
Chlamydophila caviae (former GPIC strain)
[Posted by TIGR 5/8/2003]
Chlamydophila felis genome
strain Fe/C-56
[Sequenced at Kitasato University Japan a long time ago
but not completely annotated. Available via Genbank FTP at link given].
Accessed 2/1/2008
Chlamydophila pneumoniae AR39 TIGR
Accessed 2/1/2008
Chlamydophila pneumoniae CWL029 Berkeley & Stanford
Accessed 2/1/2008
Chlamydophila
pneumoniae
genome J138: Yamaguchi and Kyushu
Universities, Japan Also
Genbank Accessed 2/1/2008
Environmental
Chlamydia genome
project, Technical University of Munich and the University of Vienna. [Mathias
Horn's group provided the first genomic sequence for an environmental
chlamydiales species, Protochlamydia
amoebophila
UWE25]. Accessed 2/1/2008
Simkania negevensis Z genome. Being sequenced by TIGR. Sequence data
still incomplete at 2/1/2008
STD Genome database
also at NMPDR [Funding
of the excellent STDGEN NIAID/NIH website finished in 2004. A real pity because
there were excellent tools available. Limited functionality still available at
the alternate link provided]. Accessed 2/1/2008
EMBL Bioinformatics proteomics
database [Select appropriate database from left
hand frame] Accessed 2/1/2008
Chlamydial proteomics database
University of Aarhus, Denmark [Includes 2D PAGE database of C.
pneumoniae VR1310 proteome and IFN-gamma induced HeLa cell proteins]
Accessed 2/1/2008
Molecular Biology (General & Bioinformatics)
Bacterial Ribosome Database : 16S ribosomal RNA sequences etc Accessed Release 9.56 2/1/2008
Bioweb
software tools: Useful sequence-related, on-line software tools Accessed
2/1/2008
Biotech : Educational resource in biotechnology, Glossary
Brookhaven
: Classic Protein structure and crystallography database. Accessed 3/1/2008
Cell signalling gateway AfCS
Nature Database of proteins and results relevant to eukaryotic cell signalling Accessed 3/1/2008
DNA
Vaccines and gene therapy (Genovac) Accessed 3/1/2008
EBI
: EMBL. UK site for gene databases and for molecular biology programs Accessed 3/1/2008
ExPASy
: Swiss Institute of Bioinformatics. Important proteomics site. Accessed 3/1/2008
LITBIO
Networked Bioinformatics Resources Accessed 3/1/2008
Molecular Biology gateway
(Horizon Press). Links to companies, protocols etc Accessed 3/1/2008
MEROPS
: Sanger Institute eptidase data base. Accessed 3/1/2008
Molecular and Cell
Biology, Immunology etc Protocols Laboratory protocols Accessed 3/1/2008
Wellcome-Sanger
Institute : Hinxton, Cambridge. Genome sequencing projects. Accessed 3/1/2008
National Center for Biotechnology information : Excellent site. Blast, Entrez, PubMed
searches etc Accessed 3/1/2008
PDBsum
: Protein databank summary, European Bioinformatics Institute, London Accessed 3/1/2008
Pfam
: Protein sequence alignments and domains. At Sanger Institute but no longer
supported beyond release 23.0 Accessed 3/1/2008
Promega
web site: Southampton based, with post grad student forum & jobs Accessed 3/1/2008
Protein
topology : Protein topology home page Accessed 3/1/2008
PROW
: Protein Reviews on the Web: Sequences and nomenclature of CD domains in
immunology Accessed 3/1/2008
SCOP
: Structural classification of proteins Accessed 3/1/2008
SDSC Biology workbench Protein
and nucleic acid search tools of San Diego Supercomputer Center Accessed 3/1/2008
TIGR
: Comprehensive microbial resource Accessed 3/1/2008
TMAP
: Membrane protein structural predictions Accessed 3/1/2008
Protein Lounge
: Human transcription factors and siRNA database Accessed 3/1/2008
Transcription factor
prediction database Accessed 3/1/2008
WIT
: Superseded by The Seed
and Puma 2. Gene function. Metabolic pathways. Accessed 3/1/2008
Science dictionaries and general reference
Biotech
life sciences dictionary [About 8,500 words]
Accessed 3/1/2008
On
Line Medical Dictionary Accessed 3/1/2008
Clinical information and resources on chlamydiae
American Medical
Association Womens Health Information [Women's
health issues including Chlamydia]
AVMA Compendium on
measures to control C. psittaci infections in birds and humans
2002 [National association of state public health
veterinarians]
BMA Board of Science and Education report on sexually transmitted diseases in
the UK, February 2002
Full document (776 Kb) ![[Acrobat]](http://www.som.soton.ac.uk/images/acrobat.gif)
European STI
Management Guidelines [Published in International Journal of STD and
AIDS 12, Supplement 3, October 2001].
International Journal of STD
and AIDS. [Joint publication of IUSTI and AGUM -
see below. Requires personal or institutional subscription to access the on-line
version].
Journal of the European Academy of Dermatology and Venerology. [In
most of Europe dermatology and venerology are combined disciplines. This is the
official Journal of the EADV. Heavily dominated by dermatology limiting its
usefulness to people interested primarily in STIs].
National strategy for sexual
health and HIV [UK Department of Health].
Full document
Sexually transmitted diseases.
Journal of the American Sexually transmitted diseases association. [Editor
is Julius Schachter, a prominent chlamydiologist. Full on-line access requires a
subscription].
Sexually transmitted infections.
[The on-line version of the journal of the same name.
Published on behalf of the BASSH. One of the key journals but full access to
papers requires an individual or institutional subscription].
UK National screening
and testing guidelines for sexually transmitted infections. STI 82,
Supplement 4 Dec 2006
[FOC registration required]
UK PHLS Guidelines for managing outbreaks of sexually transmitted
infections, July 2002
US CDC Guidelines on
screening tests to detect C. trachomatis and N. gonorrhoeae.
October 2002
US patent
office searches
[For chlamydia related patents use Multi-Find on post log
in home page].
US
STD Treatment guidelines, 1998 CDC Atlanta [For
clinicians, superseded by guidelines below]
US
STD Treatment guidelines, May 2002 CDC Atlanta [For
clinicians]
Webcast: CDC guidelines on
preventing consequences of STIs
US STD
Prevalence Report 2000 CDC Atlanta
Relevant societies
AGUM. The association for Genito Urinary Medicine. [A
specialist society providing advice and support for doctors practising genito
urinary medicine in the UK. Joint publisher with IUSTI of the International
Journal of STD and AIDS. AGUM and MSSVD are currently in merger negotiations].
Chlamydia basic research society.
[A forum for the presentation and discussion of research
on the basic biology and pathogenesis of diseases caused by chlamydiae. Primary
activity is a biennial conference. A major goal is to encourage newer people in
the field].
ISSTDR The International Society for
Sexually transmitted disease research. [The foremost
society for sexually transmitted disease research, membership is via attendance
at one of its conferences. This link gives information about the next
conference, to be held in Canada].
IUSTI. International Union against
sexually transmitted infections. [Founded in 1923 to promote international
cooperation against sexually transmitted diseases. There are active regional
branches, eg for Europe, Asia Pacific etc. The web site mainly has information
about the various IUSTI conferences and committees].
MSSVD.
Medical Society for the Study of Venereally Transmitted Diseases. [Despite
its old fashioned name, the UK based MSSVD, is one of the foremost and most
active academic societies for studying sexually transmitted infections. The web
site has some useful guidelines for people starting in genito-urinary medicine,
please details of courses and of meetings of the various groups of the society.
The society publishes the key journal Sexually transmitted infections].
Evidence based medicine sources on
chlamydial-related problems
Bandolier on
Chlamydia [Evidence based medicine study on cost
effectiveness of screening]
Chlamydia related reports in the Cochrane Collaboration Library
(abstracts)
[Updates of these abstracts may be found by searching
on update
software's web site, Oxford, UK]
Antibiotic
prophylaxis for intrauterine contraceptive device insertion
Antibiotic
regimens for endometritis after delivery
Antibiotic
for acute bronchitis
Antibiotics
in acute asthma
Antibiotics
for pre-term premature rupture of membranes
Antibiotics
for trachoma
Interventions
for encouraging sexual lifestyles and behaviours intended to prevent cervical
cancer
Interventions
for treating bacterial vaginosis in pregnancy
Interventions
for treating genital Chlamydia trachomatis infection in pregnancy
Interventions
for treating gonorrhoea in pregnancy
Macrolides
for chronic asthma
Multiple
risk factor interventions for primary prevention of coronary heart disease
Nonoxynol
9 for preventing vaginal acquisition of sexually transmitted infections by women
from men
Population-based
interventions for reducing sexually transmitted infections including HIV
Strategies
for partner notification for sexually transmitted diseases
For students
Chlamydia
lecture, Wisconsin University of Wisconsin. [For
students. Wisconsin Microbiologists are to be congratulated in making their
educational material freely available on the internet. Needs updating]
Chlamydia chapter in
textbook Becker [Students might find
this useful, but out of date]
Molecular Biology Notebook. An on line molecular biology course.
[MEW] August., 2003
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