The mira genome fragment assembler is a specialised assembler for sequencing projects classified as 'hard' due to high number of similar repeats. For EST transcripts, miraEST is specialised on reconstructing pristine mRNA transcripts while detecting and classifying single nucleotide polymorphisms (SNP) occuring in different variations thereof.

The assembly system is using iterative multipass strategies centered on usage of high confidence regions within sequences and has a fallback strategy for using low confidence regions when needed.

It features special functions to assemble high numbers of highly similar sequences without prior masking, an automatic editor that performs edits and analysis of alignments by looking at the underlying traces, detection and classification of sequence properties like SNPs with a high specificity and a sensitivity down to one mutation per sequence, possibilities to use incorrectly preprocessed sequences, routines to make use of additional sequencing information like base error probabilities and template insert sizes etc., and functions to detect and resolve possible misassemblies.

The assembler is routinely used for such various tasks as mutation detection in different cell types, similarity analysis of transcripts between organisms, and pristine assembly of sequences from various sources for oligo design in clinical microarray experiments.