Help instructions

The database portal is divided into five main sections:


BROWSE

This is the main page for data access. User is presented with list of all available entries which can be filtered using one or several filter criteria simultaneously (phiBIOTICS Family, Source Organism, Target Organism, Disease). "Reset All" button reset all filtering criteria and list of all database entries is shown.

To see a detail page for particular enzybiotics, user can either (i) use drop-down select menu to choose an enzybiotics by its abbreviated, systematic or alternative name or (ii) click enzybiotic abbreviated name in "Name" column in the table. Detail page possess two parts: (i) general biological and biochemical properties and (ii) relevant studies. If required, list of relevant studies can be filtered using four filtering criteria (Antimicrobial Agent, Study Type, Model, Administration). "Reset All" button clears all filtering and shows the list of all studies.

Question mark next to the term or dotted underline indicate tooltip help, showed when hover over the text.


TOOLS

This section provides user with possibility to use phiBiScan, a tool for prediction of potential enzybiotics. This program is based on HMMER (ver. 3.0) and scans protein sequences against local database of selected Pfam-A HMMs (Pfam 25.0) with cell wall lytic activity (Amidase_2, Amidase_3, Amidase_5, CHAP, Glucosaminidase, Glyco_hydro_19, Glyco_hydro_25, Hydrolase_2, LysM, Peptidase_M15_3, Peptidase_M23, Peptidase_U40, Phage_lysis, Phage_lysozyme, SLT, VanY). The phiBiScan input query may be either single EMBL/UniProt ID or single or multiple EMBL/UniProt/FASTA entry. If an EMBL ID (e.g., for a whole phage genome) is entered, phBiScan recognise all embedded CDSs and analyse all corresponding protein sequences. Relevance of each hit is determined by its score and E-value. The pre-set E-value threshold for the search is set to 1.0. Pfam family "Gathering threshold" is used to distinguish between significant and insignificant matches and this information is indicated in a form of coloured graphical icon in the "Score" column.

Please note, phiBiScan does not provide better or more accurate results compared to standard "full" Pfam search. However, (i) it is considerably faster (especially if analysing more sequences at once), (ii) it shows only results relevant to potential enzybiotics activity and (iii) provides greater versatility for input formats.


Any questions?

Feel free to contact the authors regarding any problems you can encounter on the phiBIOTICS portal.