miraSearchESTSNPs(1) Pipeline to discover SNPs in ESTs from different strains


The program miraSearchESTSNPs can be used for assembly of EST data from different strains (or organisms) and SNP detection within this assembly. This is the former miraEST program which was renamed as many people got confused regarding whether to use MIRA in est mode or miraEST.

miraSearchESTSNPs is a pipeline that reconstructs the pristine mRNA transcript sequences gathered in EST sequencing projects of more than one strain, which can be a reliable basis for subsequent analysis steps like clustering or exon analysis. This means that even genes that contain only one transcribed SNP on different alleles are first treated as different transcripts. The optional last step of the assembly process can be configured as a simple clusterer that can assemble transcripts containing the same exon sequence -- but only differ in SNP positions -- into one consensus sequence. Such SNPs can then be analysed, classified and reliably assigned to their corresponding mRNA transcriptome sequence. However, it is important to note that miraSearchESTSNPs is an assembler and not a full blown clustering tool.


In version 3.9.17 this functionality is deactivated.


To report bugs or ask for features, please use the new ticketing system at:


The author of the mira code is Bastien Chevreux <[email protected]>

This manual page was written by Andreas Tille <[email protected]> but can be freely used for any other distribution.