Frequently Asked Questions

1.)  About PhytAMP database
PhytAMP is a data repository of plant natural antimicrobial peptides developed by the Functional Proteomics & Alimentary Bio-preservation Research Unit at Institute of Applied Biological Sciences Tunis (ISSBAT), Tunisia in collaboration with Nutraceuticals and Functional Foods Institute (INAF), Laval University, Canada.


2.)  How to cite us?
Riadh Hammami, Jeannette Ben Hamida, Gerard Vergoten and Ismail Fliss. “PhytAMP: a database dedicated to plant antimicrobial peptides”, Nucleic Acid Research 2008, doi:10.1093/nar/gkn655


3.)  Search database
Various search creterion are available: general data, physicochemical data, structural data, taxonomy, and literature. An interactive interface allows users to add search creterion in all levels. After submission of formular results are displayed according initial view (general view, physicochemical view and structural data view). Users may switch between result interface without loss of their search results (using browse menu). To reset results, users should click on 'show all' link available in result interface.


4.)  Browse/Explore PhytAMP database
Using this feature, users may explore all content of the database. A quick search formular is provided to filter data. Users may sort results by clicking on column headers. All columns are sortable.
A specific interface was created to explore taxonomic data. The interface allows to view AMP records based on taxonomic data. Details are provided in 'Entry details'.


5.)  Homology search (Blast/Fasta/Ssearch)
Blast and Fasta Database allow users to blast/Fasta/ssearch a sequence against sequences included in the PhytAMP database.


6.)  How to identify user sequence family?
HMM models database allows to compare a user sequence against sequences included in the PhytAMP database. A score is calculated indicating to which family the user sequence may fit.


7.)  Multiple sequence alignment
Various tools are available for MSA including ClustalW, Muscle and T-Coffee.


8.)  Why register to PhytAMP database?
Anonymous users are allowed to use all sections of the database. Registration and use of PhytAMP database is completely free for all users. Registered users may also download output result tables in XLS, DOC, XML, CSV and FASTA format. In addition, with logging users may access to the list of their submitted jobs (BLAST, FASTA and SSEARCH...) and show the results. Register Now?


9.)  Submit your own sequence
Researchers in this field are invited to use the database, make suggestions and submit their peptides. All comments, queries, requests and corrections should be sent by email to administrator. Depositions of new sequence entries for naturally occurring plant antimicrobial peptides should be accompanied by a reference to a published, peer-reviewed article.