Fasta File Comparer
The Fasta File Comparer program will compare portions of the protein sequences in the source Fasta file with those in the comparison Fasta file and write the matching proteins and sequences to an output text file. The user must specify the length of residues to use when comparing the two protein files. The output file will contain the names of the proteins with residues in common, the actual residues in common, and the protein descriptions for each protein (as read from the Fasta file). The functionality of this program is a simplistic version of the BLAST algorithm where the proteins must have identical amino acid regions (rather than similar homology, which is the intent of BLAST).
See also the PepAligner program, which can read a file containing peptides and align them to a file of protein sequences (.Fasta or delimited text) using Smith-Waterman alignment.
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 | v1.1.2118 | Requirements | Microsoft NET Framework 1.1 |
| Date Updated | October 18, 2005 | File Size (Software Tool) | 180 KB (ZIP) |
| Registration Required | No | File size (Source Code) | 720 KB (ZIP) |
| Developers | Matthew Monroe | ||
| Comments | See the complete Revision History for a history of changes | ||
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.