Online Web Servers/Downloadable programs for miRNA predictions in Animal/Humans
TargetScan: TargetScan is miRNA prediction program specially designed for animals[ Mouse Worm Fly Fish]. While searching for miRNA, TargetScan takes into account the conservation of sequences across species. The webserver is very easy to use and and can predict miRNA to target and vice versa. The source code can be downloaded and run on local computer.
CID-miRNA: Designed by JNU. New delhi, this program can be used for prediction of novel miRNA precursors in human genome. Webserver has limitation on the sequence file size to 200kb. For larger files, tool can be downloaded from the website and used locally.
MiRscan : Webserver to test given hairpins are similar to experimentally verified C. elegans/C. briggsae microRNA hairpins. If you enter the sequences of two hairpins, MiRscan will assign them a score, based on their similarity to 50 pairs of experimentally verified C. elegans/C. briggsae microRNA hairpins. Not for de-novo prediction and is limited to C. elegans/C. briggsae.
miRNA - Target Gene Prediction at EMBL: This is not a server for prediction. This website provides access to their 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs. It contains predicted miRNA from Drosophila which can be downloaded from the site and used as query to find similar miRNA in other animal genomes.
miRANDA: This webserver runs miRanda program to find miRNA in selected animal genomes. miRanda is an algorithm for finding genomic targets for microRNAs. The program is written at the Computational Biology Center of Memorial Sloan-Kettering Cancer Center and the source code is available for download.
DIANA-microT program: Searches for miRNA in provided sequence. Requires a miRNA sequence and Sequence to search in. Source code not available.
MapMi: Webserver and downloadable code to search the miRNA in the given genomic sequence. Specially designed for animal genomes. The website has pretty long list of animals whose genomes can be searched. Source code is available for download.
miRBase: the microRNA database: The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download.
CID-miRNA: Designed by JNU. New delhi, this program can be used for prediction of novel miRNA precursors in human genome. Webserver has limitation on the sequence file size to 200kb. For larger files, tool can be downloaded from the website and used locally.
MiRscan : Webserver to test given hairpins are similar to experimentally verified C. elegans/C. briggsae microRNA hairpins. If you enter the sequences of two hairpins, MiRscan will assign them a score, based on their similarity to 50 pairs of experimentally verified C. elegans/C. briggsae microRNA hairpins. Not for de-novo prediction and is limited to C. elegans/C. briggsae.
miRNA - Target Gene Prediction at EMBL: This is not a server for prediction. This website provides access to their 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs. It contains predicted miRNA from Drosophila which can be downloaded from the site and used as query to find similar miRNA in other animal genomes.
miRANDA: This webserver runs miRanda program to find miRNA in selected animal genomes. miRanda is an algorithm for finding genomic targets for microRNAs. The program is written at the Computational Biology Center of Memorial Sloan-Kettering Cancer Center and the source code is available for download.
DIANA-microT program: Searches for miRNA in provided sequence. Requires a miRNA sequence and Sequence to search in. Source code not available.
MapMi: Webserver and downloadable code to search the miRNA in the given genomic sequence. Specially designed for animal genomes. The website has pretty long list of animals whose genomes can be searched. Source code is available for download.
miRBase: the microRNA database: The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download.
Online web servers and downloadable programs for miRNA prediction in plants
MiRPara: miRPara, that predicts most probable mature miRNA coding regions from genome scale sequences in a species specific manner. Authors classified sequences from miRBase into animal, plant and overall categories and used a support vector machine (SVM) to train three models based on an initial set of 77 parameters related to the physical properties of the pre-miRNA and its miRNAs. By applying parameter filtering they found a subset of ~25 parameters produced higher prediction ability compared to the full set. MiRPara software achieves an accuracy of up to 80% against experimentally verified mature miRNAs, making it one of the most accurate methods available. miRPara is a SVM-based miRNA prediction tool.
It is written in perl and can be installed on Linux, Windows and (probably) Mac. The source code is available for download at here
miRTour: miRTour is a Plant miRNA and target prediction tool available both as webserver and downloadable program.
PatScan: PatScan, also known as scan-for-matches, was an excellent piece of software writtenMark Dsouza, Niels Larsen and Ross Overbeek at Mathematics and Computer Science Division, Argonne National Laboratory in 1997 and has been extensively used by several groups to find miRNA in plant and animals. The beauty of the program is that user can specify what kind of pattern he wants to look for which in case of miRNA user will need to find hairpin structure with loop in between. The executables can be downloaded from here or source code can be downloaded from here.
It is written in perl and can be installed on Linux, Windows and (probably) Mac. The source code is available for download at here
miRTour: miRTour is a Plant miRNA and target prediction tool available both as webserver and downloadable program.
PatScan: PatScan, also known as scan-for-matches, was an excellent piece of software writtenMark Dsouza, Niels Larsen and Ross Overbeek at Mathematics and Computer Science Division, Argonne National Laboratory in 1997 and has been extensively used by several groups to find miRNA in plant and animals. The beauty of the program is that user can specify what kind of pattern he wants to look for which in case of miRNA user will need to find hairpin structure with loop in between. The executables can be downloaded from here or source code can be downloaded from here.