Mira

UNIVERSITY OF EDUCATION OKARA CAMPUNIVERSITY OF EDUCATION OKARA CAMPUSUS

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MIRA SoftWare:MIRA SoftWare:

BS-Botany 3BS-Botany 3rdrd Semester (M). Semester (M).

Class: Introduction To Computer. Class: Introduction To Computer.

Sumaria Ahmad , Roll No: 1057.Sumaria Ahmad , Roll No: 1057.

Submitted To: Sir Inam Ul Haq.Submitted To: Sir Inam Ul Haq.University Of Education Okara Campus.University Of Education Okara Campus.


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Table Of Content:Table Of Content:

IntroductionIntroductionBasic Aim Of DevelopmentBasic Aim Of DevelopmentWorking ModesWorking ModesParameters Of MiraParameters Of MiraApplicationsApplicationsConculsionConculsionReferenceReference


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Introduction:Introduction:MiraMira is a multi-pass DNA sequence data assembly program is a multi-pass DNA sequence data assembly program

(or "fragment assembler") for whole genome and EST (or "fragment assembler") for whole genome and EST projects. mira assembles reads gained by projects. mira assembles reads gained by

electrophoresis sequencing (aka Sanger sequencing), can be electrophoresis sequencing (aka Sanger sequencing), can be paired-end paired-end 454 pyrosequencing (GS20, FLX or Titanium), can be 454 pyrosequencing (GS20, FLX or Titanium), can be paired-endpaired-endSolexa sequencing (GAI or GAII, public testing phase), Solexa sequencing (GAI or GAII, public testing phase), paired-end information currently not used paired-end information currently not used

into contiguous sequences (contigs), also use the sequences of into contiguous sequences (contigs), also use the sequences of different types in a single assembly run (this is called different types in a single assembly run (this is called true true hybrid assemblyhybrid assembly..


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TheTheBasic Aim Of Its Development:Basic Aim Of Its Development:

The basic aim of its development is such as followings:The basic aim of its development is such as followings: having a full overview on the whole project at any time of the having a full overview on the whole project at any time of the

assembly, i.e. knowledge of almost all possible read-pairs in a assembly, i.e. knowledge of almost all possible read-pairs in a project, project,

using high confidence regions (HCRs) of several aligned read-pairs using high confidence regions (HCRs) of several aligned read-pairs to start contig building at a good anchor point of a contig, extending to start contig building at a good anchor point of a contig, extending clipped regions of reads on a 'can be justified' basis. clipped regions of reads on a 'can be justified' basis.

using all available data present at the time of assembly, i.e., instead of using all available data present at the time of assembly, i.e., instead of relying on sequence and base confidence values only, the assembler relying on sequence and base confidence values only, the assembler will profit from trace files containing electrophoresis signals, tags will profit from trace files containing electrophoresis signals, tags

marking possible special attributes ofmarking possible special attributes of DNA, information on specific DNA, information on specific insert sizes of read-pairs etc.insert sizes of read-pairs etc.


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Working modesWorking modes Mira has three basic working modes: genome, EST or EST-Mira has three basic working modes: genome, EST or EST-

reconstruction-and-SNP-detection. From version 2.4 on, reconstruction-and-SNP-detection. From version 2.4 on, there is only executable which supports all modes. The there is only executable which supports all modes. The name with which this executable is called defines the name with which this executable is called defines the working mode: working mode:

1. Mira1. Mira(1) for assembly of genomic data as well as assembly (1) for assembly of genomic data as well as assembly of EST data from one strain/organismof EST data from one strain/organismand and

2. MiraSearchESTSNPs2. MiraSearchESTSNPs(1) for assembly of EST data from (1) for assembly of EST data from different strains (or organisms) and SNP detection within different strains (or organisms) and SNP detection within this assembly. This is the former this assembly. This is the former miraESTmiraEST(1) program (1) program which was renamed as many people got confused regarding which was renamed as many people got confused regarding whether to use mira in est mode or miraEST. whether to use mira in est mode or miraEST.

3. Note that 3. Note that miraSearchESTSNPsmiraSearchESTSNPs(1) is usually realised as a (1) is usually realised as a link to the link to the miramira(1) executable, the executable decides by the (1) executable, the executable decides by the name it was called with which module to start. name it was called with which module to start.


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Parameters Of MIRA:Parameters Of MIRA: Parameters can be given on the command line or via parameter files. Parameters can be given on the command line or via parameter files.

Since version 2.6.0, mira knew two basic parameter types: quick Since version 2.6.0, mira knew two basic parameter types: quick switches and extensive switches. switches and extensive switches.

quick switchesquick switches, also dubbed DWIM switches (for ', also dubbed DWIM switches (for 'DDo-o-WWhat-hat-II--MMean'), ean'), are easy to use-and-combine switches activating parameter are easy to use-and-combine switches activating parameter collections for predefined tasks that will suit most people's needs. collections for predefined tasks that will suit most people's needs. Beware: due to the advent of 454, Solexa and ABI SOLiD Beware: due to the advent of 454, Solexa and ABI SOLiD technologies, these switches changes a bit since the 2.8.x series. technologies, these switches changes a bit since the 2.8.x series.

extensive switchesextensive switches offer a way to set about any possible parameter to offer a way to set about any possible parameter to configure mira for any kind of special need. While the format of configure mira for any kind of special need. While the format of extensive switches might look a little bit strange, it is borrowed from extensive switches might look a little bit strange, it is borrowed from the SGI C compiler options and allows both compact command lines the SGI C compiler options and allows both compact command lines

as well as readable and / or script generated parameter files.as well as readable and / or script generated parameter files.


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Applications:Applications:

Mira software makes it easy to make research quality Mira software makes it easy to make research quality photometric measurements of any number of stars with any photometric measurements of any number of stars with any number of standards on any number of images. Doing number of standards on any number of images. Doing ensemble photometry, plotting light curves, and reporting ensemble photometry, plotting light curves, and reporting results are a snap! results are a snap!

Use Mira software for Variable star discovery & monitoring, Use Mira software for Variable star discovery & monitoring, exoplanetexoplanet search search, milli-mag level photometry, supernova , milli-mag level photometry, supernova patrol, minor planet rotation studies. patrol, minor planet rotation studies.

Use Mira software to data mine archival science images Use Mira software to data mine archival science images available on the Web. Do hands-on analysis of terabytes of available on the Web. Do hands-on analysis of terabytes of multi-wavelength data from ground and space-based multi-wavelength data from ground and space-based instruments, as well as your own CCD images. instruments, as well as your own CCD images.

Ideal for K-12 and college astronomy education.Ideal for K-12 and college astronomy education.


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Conclusion:Conclusion:

Display, plot, animate, blink, and visually Display, plot, animate, blink, and visually enhance images in grayscale, color, and enhance images in grayscale, color, and pseudo-color. pseudo-color.

Measure high-precision coordinates, Measure high-precision coordinates, distance, angle, brightness, and statistics, distance, angle, brightness, and statistics, using both pixel units and world using both pixel units and world coordinates. coordinates.

Detect fainter objects and increase the Detect fainter objects and increase the statistical significance of measurements statistical significance of measurements using image combining and normalization using image combining and normalization techniques.techniques.


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Reference:Reference:

sourceforge.net/projects/sourceforge.net/projects/miramira--assembler/assembler/

miramira-assembler.sourceforge.net/-assembler.sourceforge.net/docs/DefinitiveGuideTodocs/DefinitiveGuideToMIRAMIRA.htm.htm

www.www.miramirametrics.com/metrics.com/miramira_al.htm_al.htm