Enteric PIPs   The Enteric server


1. Reference genome:

2. Address or gene name in the reference genome:

3. Address ranges and gene lists:
 
EccoK12: 1-4639221;   S1tm001: 1-4951371;   EccoO157: 1-5528445;   S1ty001: 1-5133713;   S1pa001: 1-4585228;   Klpn: 1-5694892;   Csak: 1-4530777;   Ciko: 1-4735357;   YrpsCO92: 1-4829855;   PsaePAO1: 1-6264404;   and S1en007: 1-4685848.   Some sequences include the plasmids.

4. Genomes to be included in the display (up to 11):

Click on the reference genome's name to skip to its corresponding genome list on this page: EccoK12, S1tm001, EccoO157, S1ty001, S1pa001, Klpn, Csak, Ciko, YrpsCO92, PsaePAO1 and S1en007.

A list of abbreviations is here. By default, the first 11 genomes are selected.

E. coli K-12 views:
EccoO157 EccoCFT73U Ecco042 EccoE2348 Shfl2a ShdyM1316 Shso53G S1tm001
S1ty001 S1pa001 S1pc001 S1en007 Klpn Ewca Ewam Srma
YrpsCO92 Yren8081 VbchO1 PsaePAO1 Csak Ciko (user)

S. typhimurium LT2 views:
S1tm002 S1tm007a S1tm007f S1ty001 S1ty002 S1pa001 S1pb001 S1pb002
S1pc001 S1en001 S1en002 S1en003 S1en007 S1du001 S1ga001 S1ga002
S1np001 S1np002 S2sa001 S3di001 S3ar001 S4ho001 S5bo001 EccoK12
EccoO157 EccoCFT73 Ecco042 EccoE2348 Shfl2a ShdyM1316 Shso53G Klpn
Ewca Ewam Srma YrpsCO92 Yren8081 VbchO1 (user)

E. coli O157:H7 views:
EccoK12 EccoCFT73 Ecco042 EccoE2348 Shfl2a ShdyM1316 ShsoG53 S1tm001
S1ty001 S1pa001 S1pc001 Klpn Ewca Ewam Srma YrpsCO92
Yren8081 VbchO1 PsaePAO1 Csak Ciko (user)

S. typhi CT18 views:
S1ty002 S1tm001 S1tm002 S1tm007a S1tm007f S1pa001 S1pb001 S1pb002
S1pc001 S1en001 S1en002 S1en003 S1en007 S1du001 S1ga001 S1ga002
S1np001 S1np002 S2sa001 S3di001 S3ar001 S4ho001 S5bo001 EccoK12
EccoO157 EccoCFT73 Ecco042 EccoE2348 Shfl2a ShdyM1316 Shso53G Klpn
Ewca Ewam Srma YrpsCO92 Yren8081 VbchO1 (user)

S. paratyphi A views:
S1pb001 S1pb002 S1pc001 S1ty001 S1ty002 S1tm001 S1tm002 S1tm007a
S1tm007f S1en001 S1en002 S1en003 S1du001 S1ga001 S1np001 S1np002
S2sa001 S3di001 S3ar001 S4ho001 S5bo001 EccoK12 EccoO157 EccoCFT73
Ecco042 EccoE2348 Shfl2a ShdyM1316 Shso53G Klpn Ewca Ewam
Srma YrpsCO92 Yren8081 VbchO1 (user)

K. pneumoniae views:
Klox S1ty001 S1ty002 S1tm001 S1tm002 S1tm007a S1tm007f S1pa001
S1pb001 S1pb002 S1pc001 S1en001 S1en002 S1en003 S1du001 S1ga001
S1np001 S1np002 S2sa001 S3di001 S3ar001 S4ho001 S5bo001 EccoK12
EccoO157 EccoCFT73 Ecco042 EccoE2348 Shfl2a ShdyM1316 Shso53G Ewca
Ewam Srma YrpsCO92 Yren8081 VbchO1 (user)

C. sakazakii views:
Ciko Ciro EccoK12 EccoO157 EccoCFT73 Ecco042 EccoE2348 Shfl2a
ShdyM1316 Shso53G S1tm001 S1ty001 S1pa001 Klpn Ewca Ewam
Srma YrpsCO92 Yren8081 VbchO1 PsaePAO1 (user)

C. koseri views:
Ciro Csak EccoK12 EccoO157 EccoCFT73 Ecco042 EccoE2348 Shfl2a
ShdyM1316 Shso53G S1tm001 S1ty001 S1pa001 Klpn Ewca Ewam
Srma YrpsCO92 Yren8081 VbchO1 PsaePAO1 (user)

Y. pestis views:
Yren8081 Csak Ciko EccoK12 EccoO157 EccoCFT73 Ecco042 EccoE2348
Shfl2a ShdyM1316 Shso53G S1tm001 S1ty001 S1pa001 Klpn Ewca
Ewam Srma VbchO1 PsaePAO1 (user)

P. aeruginosa views:
PsaePA7 PsaeLES PsaePA14 PsenL48 PsflPfO1 PsflPf5 Psmeymp PspuW619
PspuF1 PspuKT244 PsstA1501 Pssy1448A PssyB728a PssyDC300 (user)

S. enteritidis P125109 views:
S1en001 S1en002 S1en003 S1tm001 S1tm002 S1tm007a S1tm007f S1ty001
S1ty002 S1pa001 S1pb001 S1pb002 S1pc001 S1du001 S1ga001 S1ga002
S1np001 S1np002 S2sa001 S3di001 S3ar001 S4ho001 S5bo001 EccoK12
EccoO157 EccoCFT73 Ecco042 EccoE2348 Shfl2a ShdyM1316 Shso53G Klpn
Ewca Ewam Srma YrpsCO92 Yren8081 VbchO1 (user)


5. User sequence (optional). No FASTA headers, please!




Please NOTE that some queries may require more than 30s to complete.


Attention: if you use Adobe Acrobat to view these PDF files, be sure to read these instructions!
 

Description

The Enteric server produces a graphical, hypertext view of the pairwise alignments of the selected reference genome (i.e., E. coli K-12, E. coli O157:H7, S. typhimurium LT2, S. typhi CT18, S. paratyphi A, K. pneumoniae, C. sakazakii, C. koseri, Y. pestis P. aeruginosa PAO1, or S. enteritidis P125109) with several related bacteria covering 20Kb around a user-specified position or gene in the reference organism. Other organisms can be integrated as sequence data become available. For each of the compared bacteria, all significant pairwise alignments with the reference sequence in the selected region were computed with a locally developed DNA sequence alignment tool called blastz. The alignment information is displayed as a set of ``PIPs'' (Percent Identity Plots), in which positions in the reference sequence are shown along the horizontal axis and each match between the reference sequence and the other bacterial sequence is represented as a horizontal line. The percent identity of each match, a value between 50% and 100%, is then indicated by its vertical coordinate.

Additional information is embedded in each PIP. For instance, in the E. coli K-12 and O157:H7 comparative views, clicking on E. coli gene names (shown at the top of the PIP) links to their Entrez Gene classifications. Pointing at an alignment reveals the name of the contig matching that E. coli region. Colored vertical stripes at the ends of some alignments indicate the reason why that alignment terminated in the other species. Red marks sequences in the other species whose immediate neighbor has a homolog elsewhere in E. coli, and pointing at the stripe displays that other E. coli address. Blue marks sequences in the other species whose immediate neighbor has no detectable homolog in E. coli, and pointing at the stripe displays the length of the unmatched sequence. The other colored regions have no associated messages; for instance, yellow is used for regions of the reference sequence not found in the other species. Regions apparently not sequenced in the other species are marked with gray. NOTE: the significance of the color bar features for alignments in the user sequence is somewhat different. Since the sequence provided was aligned only with the 20Kb query region, and not with the entire reference genome, for performance reasons, the annotations should be interpreted with respect to that range.


Page last revised Nov 8th 2009.