PDMQ-Protein Digestion Multi Query software tool to performin silicodigestion of protein/peptide sequences

Motivation In silico enzymatic digestion tools mostly can be used for digestion of single sequence query, which means a significant limitation in their utility when a number of sequences need to be processed. The other limitation of these applications is the selection options of restriction enzymes that are usually allow only simultaneous digestion. Non-conventional proteins such as cereal prolamins require multi-enzyme multi step digestion, and for cereal proteomics experts this type of application is missing. Results PDMQ, Protein Digestion Multi Query application was developed having multi query and multi enzyme options and that way can be customized for any digestion protocol. Availability and implementation PDMQ is implemented in C# using the .NET framework and can be downloaded from http://www.agrar.mta.hu/_user/browser/File/bioinformatics/ProteinDigestion_v0_0_0_15.rar