PepSplice: cache-optimized database search for tandem mass spectraPepSplice is a tool based on fast, cache-optimized peptide database search algorithms which are essentially optimal in their use of the memory hierarchy. They only assume a parent mass constraint while the scoring scheme can be substituted. The algorithms allow to screen large search spaces including non-tryptic peptides, whole genomes, dozens of posttranslational modifications, and even unannotated point mutations and splice sites. We use an enumeration approach that allows to screen all those search spaces simultaneously while controlling the size of the overall search space. DownloadManualFile formatsCurrently, PepSplice parses simple MGF files and FASTA files (protein or DNA). Sample files are included in the download package. Source codeThe source code is written in C++ and is published under the revised BSD license. The source code is identical for Windows and Linux. Only the Makefile differs slightly. Open source licenseThe revised BSD license applies: * Copyright (c) <2007>, <Franz Roos, ETH Zurich> * All rights reserved. * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions are met: * * Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * * Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the distribution. * * Neither the name of the copyright holders nor the names of * its contributors may be used to endorse or promote products * derived from this software without specific prior written permission. * * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER ``AS IS'' AND ANY * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS BE LIABLE FOR ANY * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. CompilersPepSplice was compiled using various GCC versions from 3.32 through 4.01 on Linux, and DJGPP (a GCC-equivalent) on Windows. The source code is identical between the Linux/Mac and Windows version. The GCC compiler optimization seemed to achieve the best results on Linux Intel Pentium computers though. ContactFranz Roos Riko Jacob |
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