Category Genomics>Gene Expression Analysis/Profiling/Tools

Abstract MapMi is a computational system for automated miRNA mapping across and within species.

It is designed to locate miRNA precursor sequences in existing genomic sequences (e.g Ensembl and Ensembl Metazoa -

The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online), using potential mature miRNA sequences as input.

After searching the genome for the provided mature sequences, these hits are extended and classified taking into account major structural properties of known miRNA precursors.

The manufacturers focus on the task of mapping an identified miRNA in one species to others using both sequence similarity and RNA secondary structure.

While the manufacturers system has Not been designed for predicting the loci of novel miRNAs, it is useful to leverage the data produced by other methods, expanding it to other species.

The manufacturers approach to miRNA mapping has been demonstrated to perform well, discriminating between true miRNAs and false-positives.

The manufacturers approach is freely available as both software and a web interface.

Furthermore, the manufacturers provide precomputed mappings of all miRBase miRNA sequences across 46 Ensembl genomes and 21 Ensembl Metazoa genomes.

The manufacturers will maintain this resource through subsequent updates of miRBase, for all species available in Ensembl

MapMi Pipeline --

The MapMi pipeline works as follows:

The system is supplied with a set of input sequences corresponding to mature miRNA sequences. The user then decides which species to map these sequences against.

Note: The stand-alone version of MapMi allows the user to supply their own genomic sequence.

The genomes used have previously been processed using RepeatMasker to remove repetitive elements, that are Not similar to known miRNAs.

[RepeatMasker - RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns)].

The provided input sequences are scanned against selected genomes using the Bowtie algorithm, which is designed for efficient short sequence matching.

The system allows No gaps but up to three (3) mismatches, allowing one mismatch by default.

Each match is extended to produce a pair of potential miRNA precursors through extension of 110 nt (e.g. 70 nt 5' and 40 nt 3' and vice versa).

Each of these potential precursors is then folded using ViennaRNA. The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.

vA scoring function is used to evaluate each candidate. The scoring function takes into account both the quality of the sequence match and the structure of any predicted hairpin.

The best candidate is selected based on the score (either 5' or 3').

Candidates are further filtered according to a score-threshold. This is defined by the user, however a number of suggested thresholds are provided.

These thresholds have been selected according to an empirical analysis of true and shuffled miRNA sequences.

All miRNA precursor loci above threshold are reported to the user with their associated scores and other relevant information.

As an alternative, the user can query a database of pre-computed results, using a miRNA name as a query, and selecting the desired species and threshold.

Finally, the web version of MapMi provides further detailed analysis capabilities for precomputed results.

This includes the generation and display of Maximum Likelihood phylogenetic trees (PhyML & PhyloWidget), Multiple sequence alignments (MUSCLE & Jalview) and RNA Structural logos (RNALogo).

PhyML - PhyML is a software product that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses.

PhyloWidget - PhyloWidget is a program for viewing, editing, and publishing phylogenetic trees online. It is small, contains a simple yet advanced user interface, and contains many novel features Not available in other phylogenetic viewers.

MUSCLE - MUSCLE (multiple sequence comparison by log-expectation), is a computer program for multiple protein sequence alignment.

Elements of the algorithm include fast distance estimation using k-mer counting; progressive alignment using a profile function, called the log-expectation score, and refinement using tree-dependent restricted partitioning.

Jalview - Jalview Version 2 is a system for interactive What You See Is What You Get (WYSIWYG) editing, analysis and annotation of multiple sequence alignments.

Core features include keyboard and mouse-based editing, multiple views and alignment overviews, and linked structure display with Jmol (Jmol is an open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules).

RNALogo provides a convenient and highly configurable logo generator.

MapMi further info --

For more info about the methods behind MapMi, please read the following paper:

Guerra-Assunção, J.A. and Enright, A.J.; MapMi: Automated Mapping of miRNA loci; BMC Bioinformatics 2010, 11:133.

System Requirements

Contact manufacturer.


Manufacturer Web Site MapMi

Price Contact manufacturer.

G6G Abstract Number 20745

G6G Manufacturer Number 104154