BACTIBASE is an integrated open-access database designed for the characterization of bacterial antimicrobial peptides, commonly known as bacteriocins. The database hosts various tools for sequence analysis, such as homology search, multiple sequence alignments, Hidden Markov Models, molecular modeling and retrieval through ‘Taxonomy Browser’. For further details readers are invited to read the following papers (Hammami, et al., 2007; 2010) or visit http://bactibase.hammamilab.org.
Plants produce small cysteine-rich antimicrobial peptides (AMPs) as an innate defense against pathogens such as α-defensins, thionins, lipid transfer proteins (LTPs), cyclotides, snakins and hevein-like. PhytAMP is a database dedicated to these plant AMPs (Hammami, et al., 2009). A set of tools were provided for sequence analysis including and not limited to homology search, sequence alignments, structure prediction and hidden Markov models. PhytAMP may be accessed free of charge at http://phytamp.hammamilab.org.
SciDBMaker is stand-alone software that allows the extraction of protein data from the Swiss-Prot database, sequence analysis comprising physicochemical profile calculations, homologous sequences search, multiple sequence alignments and the building of new and more specialized databases. It compiles information with relative ease, updates and compares various data relevant to a given protein family and could solve the problem of dispersed biological search results. (Visit website)
Provides a PHP5 class for handling Blast XML