:: DESCRIPTION
ExactSearch is a web tool which enables plant biologists to search for DNA motifs in the proximal promoters, and 3′ untranslated regions of all genes from 50 genome-sequenced plant species.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
ExactSearch: a web-based plant motif search tool.
Gunasekara C, Subramanian A, Avvari JV, Li B, Chen S, Wei H.
Plant Methods. 2016 Apr 28;12:26. doi: 10.1186/s13007-016-0126-6.
:: DESCRIPTION
TAPIR is a web server designed for the prediction of plant microRNA targets. The server offers the possibility to search for plant miRNA targets using a fast and a precise algorithm. The precise option is much slower but guarantees to find less perfectly paired miRNA – target duplexes. Furthermore, the precise option allows the prediction of target mimics, which are characterized by a miRNA – target duplex having a large loop, making them undetectable by traditional tools.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bonnet, E., He, Y., Billiau, K., Van de Peer, Y. (2010)
TAPIR, a web server for the prediction of plant microRNA targets, including target mimics.
Bioinformatics 26, 1566-1568.
:: DESCRIPTION
LeafNet is a method based on a convolutional neural network (CNN) to identify plants from images of leaves.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
LeafNet: A computer vision system for automatic plant species identification
Author links open overlay panelPierreBarréaBen C.StöverbKai F.MüllerbVolkerSteinhagea
Ecological Informatics Volume 40, July 2017, Pages 50-56
:: DESCRIPTION
SplamiR is the first method for the prediction of spliced miRNAs in plants. It takes genomic sequence and the sequence of a potential target mRNA as input. In the first phase of SplamiR, a database of complementary sequence pairs is created for the given genomic sequence. These sequence pairs might encode for RNAs folding into stem-loop structures. In the second phase, this database is searched for sequences with complementarity to the given target mRNA. For the identified sequences, in silico splice variants are generated and these are classified as to whether they might represent pre-miRNAs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2011 May 1;27(9):1215-23. doi: 10.1093/bioinformatics/btr132. Epub 2011 Mar 17.
SplamiR–prediction of spliced miRNAs in plants.
Thieme CJ, Gramzow L, Lobbes D, Theissen G.
:: DESCRIPTION
P-SAMS is a web tool for the simple and automated design of artificial miRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs) for efficient and specific targeted gene silencing in plants.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
P-SAMS: a web suite for plant artificial microRNA and synthetic trans-acting small interfering RNA design.
Fahlgren N, Hill ST, Carrington JC, Carbonell A.
Bioinformatics. 2015 Sep 17. pii: btv534
:: DESCRIPTION
MIRcheck is a perl script designed to identify RNA sequences with secondary structures similar to plant miRNAs. It compares a potential miRNA and precursor against a set of secondary structure constraints derived from known plant miRNA precursors. The potential miRNA and precursor “pass” MIRcheck if all requirements are met, and “fail” MIRcheck if one or more is not.
::DEVELOPER
Bartel Lab at Whitehead Institute for Biomedical Research
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mol Cell. 2004 Jun 18;14(6):787-99.
Computational identification of plant microRNAs and their targets, including a stress-induced miRNA.
Jones-Rhoades MW, Bartel DP.
:: DESCRIPTION
PediTree is a software package to recursively analyse plant pedigree data which is arranged in a simple-single table database structure.
Peditree will lookup the parents of a variety/cultivar, then the parents of the parents (grandparents)and so on. The result is displayed in a explorer style, collapsible tree or a pedigree drawing (see images below; click to enlarge).
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Hered. 2005 Jul-Aug;96(4):465-8. Epub 2005 Apr 13.
Peditree: pedigree database analysis and visualization for breeding and science.
van Berloo R, Hutten RC.
:: DESCRIPTION
The aim of BATEx is the establishment of a data warehouse for array-based gene expression data of plants to enable experiment-spanning expression data analyses. Therefore, data is integrated from various data sources, such as BarleyBase, AtGenExpress, AFGC, TIGR SGED and IPK’s operational system FLAREX.
::DEVELOPER
the Plant Genome Resources Center (PGRC)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MultiLoc2 predicts animal, plant and fungal protein subcellularlocalizations by integrating phylogeny and Gene Ontology terms to the new version of the software.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Blum, T, Briesemeister, S, and Kohlbacher, O (2009).
MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction
BMC Bioinformatics, 10:274.