About ACANA
ACANA is an accurate and consistent alignment tool for both DNA and protein sequences. ACANA is specifically designed for aligning sequences that share only some moderately conserved regions and/or have high frequencies of long insertions or deletions. It attempts to combine the best of local and global alignments algorithms in searching for evolutionarily related regions of sequences in order to achieve the best alignment. ACANA is also robust to the small changes of alignment parameters, particularly the gap extension score. As an accurate alignment tool, ACANA is particularly useful in comparative sequence analysis for identifying conserved functional regulatory elements or functional protein domains.
Availability and Citing
- ACANA for 64-bit MacOS X (Intel CPU) [tgz] *newly released*
- ACANA for 64-bit Linux [tgz]
- ACANA for 32-bit Linux [tar] [tgz] [zip]
- ACANA for 32-bit Mac OS X (Darwin) [tar] [tgz] [zip]
- ACANA for 32-bit MS Windows (Cygwin) [tar] [tgz] [zip]
- ACANA for 32-bit Windows XP (native) [tar] [tgz] [zip]
Note: Please use a 64-bit version for aligning long sequences as a 32-bit program can use up to 4GB memory only. To uncompress files, please use one of the following commands : 1)tar xvf *.tar 2)tar xvfz *.tgz 3) unzip *.zip, then follow the instructions in the README file for installation and usage.
ACANA should be cited as
Weichun Huang, David M. Umbach, and Leping Li, Accurate anchoring alignment of divergent sequences. Bioinformatics 22:29-34, Jan 1 2006 DOI:10.1093/bioinformatics/bti772i [Abstract] [Full Text] [Supplementary-HTML] [Supplementary-PDF]
Test Data and Results
Simulated Data:The benchmark data of non-coding DNA sequences were from http://rana.lbl.gov/AlignmentBenchmarking/data.html (Pollard, Bergman, Stoye, Celniker & Eisen (2004) BMC Bioinformatics 5(1):6). The test data including the original benchmark sequences, tool alignments and performance measures can be downloaded at the links below.Actual Data: The 6007 pairs of human-mouse orthologous promoter sequences were extracted from NCBI genome database by myself according to the GenBank annotations
- Benchmark DNA sequences[sim.0.2.0.0005.tar.gz] (196MB)
- ACANA Global and Local Alignments (102MB) and Performance Measures (0.24MB)
- Avid Alignments (613MB)
- DiAlign Alignments (77MB)
- ClustalW Alignments (74MB)
- Lagan Alignments (75MB)
- Chaos Alignments [Author Recommended Parameter Settings] (7.7MB)
- BlastZ Alignments [Author Recommended Parameter Settings] (22MB)
- Human-mouse putative orthologous promoter sequences (11MB)
- ACANA Alignments (13MB)
- Avid Alignments (13MB)
- ClustalW Alignments (13MB)
- DiAlign Alignments (14MB)
- Lagan Alignments (13MB)
Note: all above files for download are in *.tar.gz format (use command 'tar xfz afile.tar.gz' to extract files). If you would like to have other data or programs used in our paper, please feel free to contact me.
Authors
ACANA was developed by Weichun Huang, under supervision of Dr. Bruce S. Weir and in collaboration with Leping Li and David M Umbach.
Copyright© 2004 Weichun Huang