miraSearchESTSNPs(1)

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.

SEE ALSO
A more extensive documentation is provided in the mira-doc package and can be found at /usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.

You can also subscribe one of the MIRA mailing lists at

    http://www.chevreux.org/mira_mailinglists.html

After subscribing, mail general questions to the MIRA talk mailing list:

    mira_talk@freelists.org

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

    http://sourceforge.net/apps/trac/mira-assembler/

AUTHOR
The author of the mira code is Bastien Chevreux <bach@chevreux.org>

This manual page was written by Andreas Tille <tille@debian.org> but can be freely used for any other distribution.