ANNOUNCEMENT: MIRA shotgun sequence assemble 1.4.0rc1

Bastien Chevreux chevreux at mbp-lserv1.inet.dkfz-heidelberg.de
Thu Mar 2 15:02:39 EST 2000


            Deutsches Krebsforschungszentrum Heidelberg
              German Cancer Research Centre Heidelberg

                           MIRA V1.4.0rc1
	        a DNA shotgun fragment assembler

                     written in 1998-2000 by
                        Bastien Chevreux


      EdIt trace file analysis and contig editing routines 
             written in 1998-2000 by Thomas Pfisterer



MIRA is a DNA shotgun sequence data assembly program capable of
assembling megabase projects which takes reads/sequences gained by (gel or
capillary) electrophoresis experiments and defined in the Staden
experiment (EXP), Sanger CAF or even FASTA file format as input and
assembles them into contigs. SCF signal electrophoresis trace files are
used, if present, to adjudicate between contradicting stretches of bases
in reads and discriminating different repeat types. The resulting assembly
is being written as standard CAF file which can easily be imported into
numerous finishing tools like GAP4.

We provide two versions of MIRA. One uses the automatic contig editor
EdIt that has been trained on standard ABI traces (mira_j), the other
version has been trained on ALF traces (mira_l).

Two additional tools are also provided with the package:
(1) scf_cut can trim SCF files
(2) convert_project can convert EXPs to CAF and FASTA; and CAF to 
    HTML format.

The canonical homepage of MIRA and EdIt, including download
possibilities, is:

            http://www.dkfz-heidelberg.de/mbp-ased/

A complete documentation can be found in the 'doc' directory of the
tarballs as HTML, texinfo and man page. Please mail suggestions,
critics, bug reports etc. to b.chevreux at dkfz-heidelberg.de
or t.pfisterer at dkfz-heidelberg.de

This will be the last release of a MIRA 1.x version except for
maintenance releases in case of heavy bugs (which we do not expect) as
work is shifting toward MIRA 2. We'd hereby like to thank the feedback
contributors from all over the world and declare open the wish list for
the next version of MIRA.

Have fun :-)
              Bastien Chevreux

-------------------------------------------------------------------------------
   Dipl.-Inform. Med. Bastien Chevreux  --  b.chevreux at dkfz-heidelberg.de 
 Deutsches Krebsforschungszentrum Heidelberg -- Abteilung Molekulare Biophysik 
    Im Neuenheimer Feld 280 -- 69120 Heidelberg -- Phone: +49 6221 42 2336
-------------------------------------------------------------------------------
    -It's mine.  =Nope, it's my one.   *CRASH*   =Alright. It WAS yours.





More information about the Bio-soft mailing list