Menteric multiple alignment   The Menteric server


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

Reference genome:

Address or gene name in the reference genome:

Address ranges: ECO: 1-4639221, STM: 1-4951371, ECH: 1-5528445, STY: 1-5133713, SPA: 1-4585228, KPN: 1-5694892 and ESA: 1-4530777. The STY, STM, KPN and ESA sequences include the plasmids.

The complete gene lists for the reference genomes are here (ECO, STM, ECH, STY, SPA, KPN, ESA).
 

Conservation criterion for drawing the conserved regions in the alignment:

Types of functional sites in the display:       Genes     Promoters     Proteins binding sites
 

Genomes to be included in the display (up to 11). A list of abbreviations is here. By default, the first 11 genomes will be selected.

E. coli K-12 views:
          ECH ECU ECA ECP SHG SHD SHS STM STY SPA SPC
          KPN ERC ERA SMA YPE YEN VCH PAE ESA CKO (user)

S. typhimurium LT2 views:
          SSL STA STF STY STT SPA SPB SPR SPC SEP SEN SEB
          SDU SGA SNE SNL SSA SDI SAR SHO SBO ECO ECH ECU
          ECA ECP SHG SHD SHS KPN ERC ERA SMA YPE YEN VCH (user)

E. coli O157:H7 views:
          ECO ECU ECA ECP SHG SHD SHS STM STY SPA SPC
          KPN ERC ERA SMA YPE YEN VCH PAE ESA CKO (user)

S. typhi CT18 views:
          STT STM SSL STA STF SPA SPB SPR SPC SEP SEN SEB
          SDU SGA SNE SNL SSA SDI SAR SHO SBO ECO ECH ECU
          ECA ECP SHG SHD SHS KPN ERC ERA SMA YPE YEN VCH (user)

S. paratyphi A views:
          STY STT SPB SPR SPC STM SSL STA STF SEP SEN SEB
          SDU SGA SNE SNL SSA SDI SAR SHO SBO ECO ECH ECU
          ECA ECP SHG SHD SHS KPN ERC ERA SMA YPE YEN VCH (user)

K. pneumoniae views:
          KOX STY STT STM SSL STA STF SPA SPB SPR SPC SEP
          SEN SEB SDU SGA SNE SNL SSA SDI SAR SHO SBO ECO
          ECH ECU ECA ECP SHG SHD SHS ERC ERA SMA YPE YEN
          VCH (user)

Enterobacter sakazakii views:
          CKO ECO ECH ECU ECA ECP SHG SHD SHS STM STY
          SPA KPN ERC ERA SMA YPE YEN VCH PAE (user)
 

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




Output format:       PostScript     PDF

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


Color coding for alignment underlays:

Light Chocolate  -- Genes (ORFs); Green  -- Promoters; Red  -- Protein Binding Sites.



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 or E. sakazakii) 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 and E. sakazakii ATCC BAA-894 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 Jun 29th, 2008.