:: DESCRIPTION
Bamseek provides easy-to-use user interface to browse files too large to be opened with conventional text editors, such as TextEdit or Word. Supports SAM/BAM, VCF (BGZF-compressed and uncompressed), and FASTQ formats.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
ParaSAM is a high performance parallel processing implementation of the SAM (Significance Analysis of Microarrays) algorithm. The permutations are divided across the multiple nodes. The computational workload is divided among multiple CPUs and the main memory of all participating computers is utilized to avoid caching operations to the disk, which significantly decrease algorithm execution time.
::DEVELOPER
Ashok Sharma & Richard A. McIndoe, Ph.D.
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
If you don’t want to install ParaSAM locally, you can use a Web version here.
If you make use of the program presented here, please cite the following article:
Sharma A, Zhao J, Podolsky R, McIndoe RA: ParaSAM: A parallelized version of the significance analysis of microarrays algorithm. Bioinformatics 2010.
:: DESCRIPTION
After doing a SAM analysis, you will want a more visual representation, or want to see if there is even more detailed substructure within these genes by using Cluster. Samster will take an Excel spreadsheet or text files and extract the raw data into a text output file, which can be fed directly into Cluster or opened in Treeview. Samster circumvents the need to create databases each time you wish to accomplish this task.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
Samster for Win ; Source Code ; Manual ; Sample input file
:: MORE INFORMATION
The software is copyrighted under the terms of the GNU General Public License. You can view this license at http://www.gnu.org/licenses/gpl.txt.
If you use SAMster, please cite:
Mueller A, O’Rourke J, Chu P, Kim CC, Sutton P, Lee A, Falkow S.
Protective immunity against Helicobacter is characterized by a unique transcriptional signature.
Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12289-94.