MIRA – Methylation-based Inference of Regulatory Activity

MIRA

:: DESCRIPTION

The MIRA package aggregates DNA methylation across the genome for instances of a genomic feature like histone ChIP peaks, transcription factor ChIP peaks, or open chromatin regions in order to give a single signature and score for that feature, which may be used to infer regulatory activity.

::DEVELOPER

Sheffield lab of computational biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
R

:: DOWNLOAD

MIRA

:: MORE INFORMATION

Citation

Lawson JT, Tomazou EM, Bock C, Sheffield NC.
MIRA: an R package for DNA methylation-based inference of regulatory activity.
Bioinformatics. 2018 Aug 1;34(15):2649-2650. doi: 10.1093/bioinformatics/bty083. PMID: 29506020; PMCID: PMC6061852.

MIRA 4.9.6 – Whole Genome Shotgun and EST Sequence Assembler

MIRA 4.9.6

:: DESCRIPTION

MIRA (Mimicking Intelligent Read Assembly)is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads). It can be seen as a Swiss army knife of sequence assembly developed and used in the past 12 years to get assembly jobs done efficiently – and especially accurately. That is, without actually putting too much manual work into finishing the assembly.

::DEVELOPER

Bastien Chevreux

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac OsX

:: DOWNLOAD

MIRA

:: MORE INFORMATION

Citation:

Chevreux et al. (2004)
Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs
Genome Research 2004. 14:1147-1159.

miRA 1.2.0 – micro RNA Identification tool

miRA 1.2.0

:: DESCRIPTION

miRA is a new tool to identify miRNA precursors in plants, allowing for heterogeneous and complex precursor populations.

::DEVELOPER

Michael Huttner

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX

:: DOWNLOAD

miRA

:: MORE INFORMATION

Citation

miRA: adaptable novel miRNA identification in plants using small RNA sequencing data.
Evers M, Huttner M, Dueck A, Meister G, Engelmann JC.
BMC Bioinformatics. 2015 Nov 5;16:370. doi: 10.1186/s12859-015-0798-3.