While I don’t consider myself a programmer, I do know just enough to be dangerous, and have on occasion written simple programs. These are generally related to my research interests, and were designed based on a previous lack of such programs to general (PC) users such as myself. I have several programs available here. These are all stand alone executables designed using Visual Basic.
The first program I developed is designed for MALDI searches of trypsin digested proteins, for protein identification. As part of my graduate work, I ran a number of experiments to identify different proteins expressed under various conditions, and did some work with Dr. Martha Medina to identify these proteins from the organism Nitrosomonas europaea. The principle problem we found was that most databases did not contain all of the proteins from this organism, and since the genome sequence was available, and thus all the proteins from this organism were known, it seemed rather redundant to perform searches against proteins from other organisms. Thus, I wrote this computationally intensive program to search all protein in a specific genome for specific peaks identified using MALDI. I was rather amazed at the time that nothing like this was available. As with all my programs, there is no help file. Should you have questions, you may feel free to contact me. All these programs are referenceware, meaning, should you use them, I would ask only that you acknowledge the program and me. The file is downloaded as an executable, and thus, using internet explorer, you must right click (PC users), and then click on Save Target As.
The second program I have available here is designed to search for sequences of redundancy in proteins, also known as internal repeats. There are a number of classes of repeat proteins that are known, and one of the proteins I worked on during my graduate work was rather interesting to me, based on the rather simple sequence it was based upon. This protein was found to bind multiple metals, and was thus given the name Small Metal Binding Protein (SMBP). It is intriguing, because the protein is simply a scaffold of ten sets of seven residue repeats (in brackets), as shown here;
Based on this protein, I wanted to search for other proteins in this organism that used the same evolutionary tactic of a seven residue repeat unit to prepare a simple scaffold in a manner similar to SMBP. This simple program, is specific for such proteins, and analyzes each protein using seven residue segments, to look for the highest scoring repeated sequence in the protein. Using a sliding window approach, and similarity matrices to score seven residue segments against the parent segment, it will yield the highest scoring seven residue segment, and all other sequences in the specific protein that meet the similarity requirements. Though significantly slower than other programs available for internal protein repeats, it is designed for easy manipulation of search requirements by allowing the user to easily change the scoring for the matrix (i.e., to bias for repeats containing histidine). The file is downloaded as an executable, and thus, using internet explorer, you must right click (PC users), and then click on Save Target As.
I am also providing the current databases of proteins identified to contain these characteristics from the more than 100 species of bacteria and archae that were analyzed using this program. These may be downloaded as the text files in FASTA format, and are best viewed using a font such as Courier, which gives each character equal spacing.