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Database Search Help

  1. Browse Terminators in Genomes by Alphabet - eg, if you want to get the data for all Escherichia coli genomes, you can click on "E".
  2. Calculated under two parameter set - for every genome sequence, data has been computed using two sets of parameters. (1) Stem length is set between 4-12bp, Loop size is set between 3-8nt. (2) Stem length is set between 4-30bp. Loop size is set between 3-9nt. When you reach a genome, you will find links to both sets side-by-side.
    Example: Haemophilus influenzaei Rd KW20, complete genome. ||4.12:3.8:3:270 || ||4.30:3.9:3:270 || enter as per your choice.
  3. Stem length - you can set the range at either between 4 and 12 or 4 and 30.
  4. Loop length - you can set the range either between 3 and 9 or 3 and 8.
  5. Max. mismatch and distance from ORF- fixed at 3 and 270, respectively.
  6. Organism name - type in name of genus or species.
  7. ΔG cut off, genome length, %GC content, total ORFs, total terminators, terminators (greatest ΔG), etc. - one or more than one of these parameters can be inputted to fine-tune your search.
    Example: >65 (%GC content) shows all genomes which have a genomic GC content higher than 65%.
    Example: >65% (GC content) AND >6000 (Total ORFs) shows all genomes which both genomic GC content higher than 65% a s well as more than 6000 genes.
    Example: entering >500 (Total U type) gives genomes which have more than 500 U-shaped or tandem terminators.
  8. Total terminators - number of hairpins identified in a genome (described as ALL in text).
  9. Total terminators (greatest ΔG) - number of hairpins with most negative ΔG value (described as "Best" terminator candidates in text. Best is a subset of ALL. If a gene has >1 hairpin downstream of its stop codon, the hairpin with the most negative ΔG value is considered the "Best" terminator candidate. Please see text)
  10. Taxon identifier - enter the taxon ID as provided by NCBI. The taxon ID of several bacterial phyla and classes is provided below.
    Example: entering taxon ID for gammaproteobacteria shows all genomes of that class only.
    Proteobacteria - 1224 - subdivided into CLASSES - alpha (28211), beta (28216), gamma (1236), delta (28221), epsilon (29547)
    Actinobacteria -201174
    Firmicutes - 1239 subdivided into CLASSES - bacilli (91061), clostridium (186801)
    Fibrobacteres - 65842
    Bacteriodetes - 976
    Chlorobi - 1090
    Chylamidae - 204428
    Spirochaetes - 203691
    Chloroflexi - 200795
    Thermotogae - 200918
    Cyanobacteria - 1117
    Planctomycetes - 203682
    Fusobacteria - 32066
    Deinococcus-Thermus - 1297
    Tenericutes - 544448
    Aquificae - 200783
  11. Plasmids - Cases where no terminators are detected show a NULL (all values zero) page.