Menteric multiple alignment   The Menteric server


This produces a 1000bp long alignment starting at a given location.

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. Conservation criterion for drawing the conserved regions in the alignment:

5. Types of functional sites in the display:       Genes     Promoters     Protein binding sites

6. 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 will be 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)

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

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

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

Pseudomonas 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)

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




Output format:       PostScript     PDF

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



Description

The Menteric web server computes and displays nucleotide-level multiple alignments of sequences from several related genomes in a 1Kb region starting at the user-specified address, or centered about the start site of the user-supplied gene. The alignment is rendered as a PostScript or PDF document in which annotations of ORFs, promoters and protein binding sites in the reference (i.e., E. coli K-12 or O157:H7, S. typhimurium LT2, S. typhi CT18, S. paratyphi A, K. pneumoniae, C. sakazakii, C. koseri, Y. pestis, P. aeruginosa or S. enteritidis P125109) genome are color-coded. Conserved regions, potentially associated with functional sites, are surrounded by boxes.

Regulatory site annotations for E. coli K-12 were extracted from the GenBank annotation version M54 (Blattner et al, 1997), while gene information for E. coli K-12, E. coli O157:H7, S. typhimurium LT2, S. typhi CT18, C. sakazakii ATCC BAA-894, P. aeruginosa PAO1 and S. enteritidis P125109 was parsed from the gene tables in the Entrez Genomes section. The lists of S. paratyphi A and K. pneumoniae genes were obtained from the Genome Sequencing Center at the Washington University, St. Louis (WUSTL). In addition to functional landmarks, the user can select from several types of conservation criteria for identifying conserved regions to be displayed. By default, regions longer than 6 nucleotides in which all columns have a letter agreement better than 80% are reported as conserved.

When the output is displayed as a PDF document, the annotation labels contain embedded links to various data repositories available on the web. In the comparative views, clicking on a gene's name leads to its entry in the Entrez Gene repository, and promoter and protein binding site labels are links to the source of annotation data, where available. Clicking on the sequence name on the right-hand side of the alignment downloads a web page containing the contig's sequence data in the alignment range.

In the display, promoter regions are shown in green, protein binding sites in red, and genes (ORF's) in light chocolate. The label ``PR'' above a green promoter band specifies that no experimental evidence has yet been found for it (hence, it is a predicted promoter), and ``+1'' marks the start of transcription. An abbreviation for the species name is indicated at the right end of each line.

List of abbreviations.
 


Page last revised Nov 8th 2009.