PDMQ- Protein Digestion Multi Query software tool to perform in silico digestion 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