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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.
The package provides the following executables: Binaries provided: * mira: for assembly of genome sequences * miramem: estimating memory needed to assemble projects. Realised through link to mira. * convert_project: for converting project file types into other types * caf2fasta, caf2gbf, caf2text, caf2html, gbf2caf and gbf2fasta are some frequently used file converters (realised through links to convert_project) * scftool: set of tools useful when working with SCF trace files * fastatool: set of tools useful when working with FASTA trace files
Scripts provided: * fasta2frag.tcl: fragmenting sequences into smaller, overlapping subsequences. Useful for simulating shotgun sequences. Can create subsequences in both directions (/default) and also paired-end sequences. * fastaselect.tcl: given a FASTA file (and possibly a FASTA quality file) and a file with names of reads, select the sequences from the input FASTA (and quality file) and writes them to an output FASTA * fastqselect.tcl: like fastaselect.tcl, only for FASTQ * fixACE4consed.tcl: Consed has a bug which incapacitates it from reading consensus tags in ACE files written by the MIRA assembler (and possibly other programs). This script massages an ACE file so that consed can read the consensus tags.
Rheinfelden, Summer 2011 MIRA version 3.4.x MIRA - The Genome and EST Sequence Assembly System EdIt - An Automatic Assembly Editing Tool License ======= Since version 2.8.0, MIRA (and the therein contained version of EdIt) is licensed under the open source GPL v2 license. please consult the "COPYING" file for more information on the GPL. more»
Files in this directory are meant as help for supporting interaction with other genomic software. Currently, only a small definition file for defining tags in the Staden package (GAP4) and the consed package are present, but this section should grow. Files included: For the STADEN package: GTAGDB For the gap4 package, so that it knows the tags used by mira, miraEST and EdIt For the more»
License change ============== Since version 2.8.0, MIRA (and the therein contained version of EdIt) is licensed under the open source GPL v2 license. please consult the "COPYING" file for more information on the GPL. For a list of changes, please consult the "CHANGES.txt" file which is located in the top level binary package distributions or in src/mira of source code distributions.
mira (220.127.116.11-3) unstable; urgency=low [ Charles Plessy ] * Build-depend on libgoogle-perftools more»
Big thanks to Sandor Suhai, Karl-Heinz Glatting and Frieder Kern from the german cancer research ce more»