:: DESCRIPTION
ThermonucleotideBLAST is a software program for searching a target database of nucleic acid sequences using an assay specific query.
::DEVELOPER
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Wolfgang Ludwig, et al.
ARB: a software environment for sequence data.
Nucleic Acids Research. 2004. 32(4):1363-1371.
:: DESCRIPTION
Targetfinder predicts small RNA targets in a sequence database using a plant-based scoring metric.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, Carrington JC. (2007)
High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes.
PLoS ONE 2, e219.
:: DESCRIPTION
Oligomap is a program for fast identification of nearly-perfect matches of small RNAs in sequence databases. It allows to exhaustively identify all the perfect and 1-error (where an error is defined to be a mismatch, insertion or deletion) matches of large sets of small RNAs to target sequences. Optimal performance is achieved at about 500000 query sequences
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Berninger P, Gaidatzis D, van Nimwegen E, Zavolan M.
“Computational analysis of small RNA cloning data“,
Methods, 44(13-21), 2008
