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miraSearchESTSNPs - Online in the Cloud

Run miraSearchESTSNPs in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command miraSearchESTSNPs that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


miraSearchESTSNPs - Pipeline to discover SNPs in ESTs from different strains

DESCRIPTION


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.

SYNOPSIS


In version 3.9.17 this functionality is deactivated.

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