
General
The available information for over 4000 strains represented by 16S rRNA sequences, much of which cannot be shown in the phylogenetic tree owing to space limitation, is presented in a single large table containing 17 fields.
Searching
Using the search function is quite simple.
The strain data are presented in columns. Type or paste a search expression in the relevant search box, multiple boxes may be used sequentially or simultaneously; records that do not contain the term(s) are hidden, the positive records remaining visible. When finished, delete the expression with the ′Reset′ button to re-show the whole table.
The search term is case insensitive, and may be a whole or partial word. Thus (taking the generic name Gloeobacter as an example):
′gloeob′, ′gloeobacter′ or ′Gloeobacter′ (without the tick marks) find all strains of the genus, whereas ′gloeo′ finds additional genera such as Gloeothece, Gloeocapsa... whose name starts with that term.
The dropdown menus
For genome size, the data are presented for strains represented by complete genome sequences only, the rest being shown as ′n/a′ because we cannot be certain of the size of draft genomes, and many strains are represented by 16S rRNA sequences obtained by specific PCR. A dropdown menu permits the choice of searching for values greater than, equal to, or less than, a chosen size.
Although the G+C content of the 16S rRNA gene varies little across the tree, a dropdown menu is provided to permit the same choices as those described above for complete genome sequences.
The same choices may also be made for the start position (given as position in the alignment), using the rRNA start dropdown; this function shows that many sequences start after position 700 of the alignment, which is currently 2408 nt long. However, start position depends on the primers chosen for PCR , which are often not wisely chosen.
The length of the 16S rRNA gene varies directly with the start position, and a dropdown menu is therefore not provided.
Print or copy
The results may be printed via the ′print′ option of the browser; landscape and tabloid paper size are best for this wide table. Even if the page has been scrolled, the search box and search term are visible in the printed version. However, the resulting PDF is difficult to read and manipulate. It is more convenient to save the results of a search (which will contain fewer rows); this may be done simply by selecting the rows of interest, copying/pasting into a spreadsheet programme, deleting the unwanted page header part and removing any unwanted columns.