VectorEditor 1.8.1
:: DESCRIPTION
VectorEditor is an open source, cloud-based freely open-source visual DNA editing and annotation tool.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
- Web browser
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
VectorEditor is an open source, cloud-based freely open-source visual DNA editing and annotation tool.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Possum predicts cis-elements in DNA sequences using the standard method of Position Specific Scoring Matrices. It measures the resemblance of every sequence fragment to the chosen cis-element matrices by calculating log-likelihood ratio scores (base e), and returns high-scoring sequence fragments.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W420-3.
MotifViz: an analysis and visualization tool for motif discovery.
Fu Y, Frith MC, Haverty PM, Weng Z.
:: DESCRIPTION
Cister (Cis-element Cluster Finder) predicts regulatory regions in DNA sequences by searching for clusters of cis-elements.
::DEVELOPER
:: SCREENSHOTS
Command Line
Web version:
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Frith, M. C., Hansen U. and Weng, Z.
Detection of cis-element clusters in higher eukaryotic DNA
Bioinformatics 2001 Oct;17(10):878-889.
:: DESCRIPTION
ROVER (Relative OVER-abundance of cis-elements) is a tool for determining if one or more of a group of transcription factors is likely to regulate a group of genes. It was designed for use with promoters from groups of genes that are suspected of being co-regulated, such as those from a microarray study. ROVER compares two groups of promoters (a suspected co-regulated group and a non-regulated group) by determining the relative over-abundance of likely binding sites for a particular Transcription Factor (TF) in one group versus the other. ROVER calculates the significance of any over-abundance of binding sites for each TF and reports a probability of its chance occurrence. This can be interpreted as the probability that a given TF regulates the group of genes in question. Likely binding sites are found by looking for high-scoring matches to a Position Specific Weight Matrix (PSSM), which represents known binding sites for a transcription factor. In addition to determining the significance of each TF, ROVER also provides the subset of sequences likely to be regulated by each TF and the specific significant binding sites.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Haverty, PM., Hansen, U., Weng, Z. (2004) Computational Inference of Transcriptional Regulatory Networks from Expression Profiling and Transcription Factor Binding Site Identification. Nucleic Acids Research, Vol. 32, 179-188.
:: DESCRIPTION
Clover (Cis-eLement OVERrepresentation) is a program for identifying functional sites in DNA sequences. If you give it a set of DNA sequences that share a common function, it will compare them to a library of sequence motifs (e.g. transcription factor binding patterns), and identify which if any of the motifs are statistically overrepresented in the sequence set.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Martin C Frith, Yutao Fu, Liqun Yu, Jiang-Fan Chen, Ulla Hansen, Zhiping Weng (2004). Detection of functional DNA motifs via statistical over-representation. Nucleic Acids Research 32(4):1372-81.
:: DESCRIPTION
LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.
::DEVELOPER
Miller Lab at Penn State University Center for Comparative Genomics and Bioinformatics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Harris, R.S. (2007)
Improved pairwise alignment of genomic DNA.
Ph.D. Thesis, The Pennsylvania State University.
:: DESCRIPTION
CodonCode Aligner is a program for sequence assembly, contig editing, and mutation detection, available for Windows and Mac OS X. Aligner is compatible with Phred-Phrap and fully supports sequence quality scores, while offering a familiar, easy-to-learn user interface.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
4Peaks helps molecular biologists to visualize and edit their DNA sequence trace 4Peaks renders your traces sharper, automatically translate your sequences, reads the most common sequence file formats, displays important sequence quality data too.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MySSP is a program for the simulation of DNA sequence evolution across a phylogenetic tree
::DEVELOPER
Michael S. Rosenberg’s Laboratory
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Rosenberg, M.S. (2005)
MySSP: Non-stationary evolutionary sequence simulation, including indels.
Evolutionary Bioinformatics Online 1:81–83
:: DESCRIPTION
EDSSI is an online bioinformatics pipeline that checks for syntax errors through three steps. First, ORF prediction in input DNA sequences is done by GeneMark; next, homologous sequences are retrieved by BLAST; and finally, syntax errors in the protein sequence are predicted by using the SIFT algorithm.
:: DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
ACS Synth Biol. 2014 Feb 21;3(2):91-6. doi: 10.1021/sb400176e. Epub 2014 Jan 3.
Engineered DNA sequence syntax inspector.
Hsiau TH1, Anderson JC.