PepAligner
The PepAligner program can read a file containing peptides and align them to a file of protein sequences (.Fasta or delimited text) using Smith-Waterman alignment. The output file will show the original peptide along with the regions of proteins that align well with the peptide (see below for examples).
Please see the Command Line Application Help page for additional information on running this program at the Windows command prompt.
| Download Software Tool | Download Source Code |
| Version | v1.0.2895 | Requirements | Microsoft NET Framework 1.1 |
| Date Updated | December 5, 2007 | File Size (Software Tool) | 173 KB (ZIP) |
| Registration Required | No | File size (Source Code) | 659 KB (ZIP) |
| Developers | Matthew Monroe | ||
| Comments | See the complete Revision History for a history of changes | ||
Example Data Files
Input Peptides
LRDKLQLVGDDLFVTNTK MQQQCATLADLAVGTAAGQLK WTSAVLGAAGLGGQALALLLK WWFMREHWLLACEDSSLEEAKR FNNAAACTLADLAVGTAAGKLK VVVLGGGDTAMDMKR WRWRRNWYWHEFESRDTYWR WLDAVTAAGVEVAK WHWHWYHHPENLYNNGKTPDR WWWWFVTPWFGMSGTLLYMTR WWYVTADGFCSSGDGTDWSTYK
Output using a Shewanella .Fasta file
Detailed Example Input and Output Files
- Example input file -- List of peptides
- Example fasta file excerpt -- 40 proteins from Shewanella oneidensis
- Example output file -- Tab-delimited file of results
Acknowledgment
All publications that utilize this software should provide appropriate acknowledgement to PNNL and the OMICS.PNL.GOV website. However, if the software is extended or modified, then any subsequent publications should include a more extensive statement, using this text or a similar variant:
Portions of this research were supported by the NIH National Center for Research Resources (Grant RR018522), the W.R. Wiley Environmental Molecular Science Laboratory (a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at PNNL), and the National Institute of Allergy and Infectious Diseases (NIH/DHHS through interagency agreement Y1-AI-4894-01). PNNL is operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC05-76RL0 1830.