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identify members of gene families.

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or a DNA sequence to another DNA sequence or a DNA library.
ssearch
performs a rigorous Smith-Waterman alignment between a protein sequence
and another protein sequence or a protein database.
fastx/fasty
compare a DNA sequence to a protein sequence database, translating
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prfx/prss
evaluate the significance of pairwise similarity scores using a Monte Carlo analysis.</description>
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identifying local duplications within a sequence. Other programs provide information
on the statistical significance of an alignment. Like BLAST, FASTA can be used to
infer functional and evolutionary relationships between sequences as well as help
identify members of gene families.

FASTA includes:

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compares a protein sequence to another protein sequence or to a protein database,
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ssearch
performs a rigorous Smith-Waterman alignment between a protein sequence
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fastx/fasty
compare a DNA sequence to a protein sequence database, translating
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on the statistical significance of an alignment. Like BLAST, FASTA can be used to
infer functional and evolutionary relationships between sequences as well as help
identify members of gene families.

FASTA includes:

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compares a protein sequence to another protein sequence or to a protein database,
or a DNA sequence to another DNA sequence or a DNA library.
ssearch
performs a rigorous Smith-Waterman alignment between a protein sequence
and another protein sequence or a protein database.
fastx/fasty
compare a DNA sequence to a protein sequence database, translating
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Debug information is useful when developing applications that use this
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  <description>This package provides debug information for package SHRiMP.
Debug information is useful when developing applications that use this
package or when debugging this package.</description>
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  <description>This package provides debug sources for package SHRiMP.
Debug sources are useful when developing applications that use this
package or when debugging this package.</description>
  <packager/>
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  <description>This package provides debug sources for package SHRiMP.
Debug sources are useful when developing applications that use this
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absent from previous genome assemblies.</description>
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    <rpm:vendor>openSUSE Build Service</rpm:vendor>
    <rpm:group>Development/Debug</rpm:group>
    <rpm:buildhost>build21</rpm:buildhost>
    <rpm:sourcerpm>muscle-3.8.31-1.3.src.rpm</rpm:sourcerpm>
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  </format>
</package>
<package type="rpm">
  <name>muscle-debuginfo</name>
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  <summary>Debug information for package muscle</summary>
  <description>This package provides debug information for package muscle.
Debug information is useful when developing applications that use this
package or when debugging this package.</description>
  <packager/>
  <url>http://www.drive5.com/muscle</url>
  <time file="1291551094" build="1291551072"/>
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<location href="x86_64/muscle-debuginfo-3.8.31-1.3.x86_64.rpm"/>
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</package>
<package type="rpm">
  <name>perl-Bio-Graphics</name>
  <arch>i586</arch>
  <version epoch="0" ver="2.14" rel="3.33"/>
  <checksum type="sha" pkgid="YES">785d60062053752ee45350df309b4cda801dde0c</checksum>
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  <description>Bio::Graphics::Panel - Generate GD images of Bio::Seq objects</description>
  <packager/>
  <url>http://search.cpan.org/dist/Inline-CPP/</url>
  <time file="1351851487" build="1351851468"/>
  <size package="590842" installed="1463883" archive="1501372"/>
<location href="i586/perl-Bio-Graphics-2.14-3.33.i586.rpm"/>
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    <rpm:license>same terms as Perl</rpm:license>
    <rpm:vendor>openSUSE Build Service</rpm:vendor>
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      <rpm:entry name="perl(Bio::Graphics::Glyph::rndrect)"/>
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      <rpm:entry name="perl(Bio::Graphics::Glyph::three_letters)"/>
      <rpm:entry name="perl(Bio::Graphics::Glyph::tic_tac_toe)"/>
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    <file>/usr/bin/render_msa.pl</file>
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    <file>/usr/bin/glyph_help.pl</file>
    <file>/usr/bin/search_overview.pl</file>
    <file>/usr/bin/frend.pl</file>

  </format>
</package>
<package type="rpm">
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  <arch>src</arch>
  <version epoch="0" ver="2.14" rel="3.33"/>
  <checksum type="sha" pkgid="YES">c4a7f0cdee46b0de6cdac34739980adfb872ac5d</checksum>
  <summary>Bio::Graphics::Panel - Generate GD images of Bio::Seq objects</summary>
  <description>Bio::Graphics::Panel - Generate GD images of Bio::Seq objects</description>
  <packager/>
  <url>http://search.cpan.org/dist/Inline-CPP/</url>
  <time file="1351851488" build="1351851468"/>
  <size package="784014" installed="782098" archive="782496"/>
<location href="src/perl-Bio-Graphics-2.14-3.33.src.rpm"/>
  <format>
    <rpm:license>same terms as Perl</rpm:license>
    <rpm:vendor>openSUSE Build Service</rpm:vendor>
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      <rpm:entry name="perl(GD)"/>
      <rpm:entry name="perl(ExtUtils::MakeMaker)"/>
      <rpm:entry name="perl(Statistics::Descriptive)"/>
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      <rpm:entry name="perl(GD::SVG)"/>
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    <rpm:recommends>
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    </rpm:recommends>

  </format>
</package>
<package type="rpm">
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  <summary>Bio::Graphics::Panel - Generate GD images of Bio::Seq objects</summary>
  <description>Bio::Graphics::Panel - Generate GD images of Bio::Seq objects</description>
  <packager/>
  <url>http://search.cpan.org/dist/Inline-CPP/</url>
  <time file="1351851951" build="1351851937"/>
  <size package="590846" installed="1463883" archive="1501376"/>
<location href="x86_64/perl-Bio-Graphics-2.14-3.33.x86_64.rpm"/>
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    <rpm:license>same terms as Perl</rpm:license>
    <rpm:vendor>openSUSE Build Service</rpm:vendor>
    <rpm:group>Development/Libraries/Perl</rpm:group>
    <rpm:buildhost>build12</rpm:buildhost>
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hash and an object-oriented interfaces. It provides the ability to read fields from
SCF files and limited ability to modify them and write them back.</description>
  <packager/>
  <url>http://search.cpan.org/dist/Bio-SCF/</url>
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hash and an object-oriented interfaces. It provides the ability to read fields from
SCF files and limited ability to modify them and write them back.</description>
  <packager/>
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Debug sources are useful when developing applications that use this
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SAM (Sequence Alignment/Map) format is a generic format for storing large
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SAM (Sequence Alignment/Map) format is a generic format for storing large
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SAM Tools provide various utilities for manipulating alignments in the SAM
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a per-position format.</description>
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    <file>/usr/lib/debug/usr/bin/tophat_reports.debug</file>
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  <description>This package provides debug sources for package tophat.
Debug sources are useful when developing applications that use this
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  <url>http://tophat.cbcb.umd.edu</url>
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  <url>http://tophat.cbcb.umd.edu</url>
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  <description>VAAL is a variant ascertainment algorithm that can be used to detect SNPs, indels, and more complex
genetic variants. On bacterial data sets, it achievies very high sensitivity, and near perfect
specificity. VAAL can be used to compare reads from one strain to a reference sequence from another
strain. It can also be used to compare reads from two strains to each other, using a third strain
to determine homology. For example, we have used VAAL to find a single mutation responsible for
bacterial resistance: the output of the program was that single mutation and no others.
VAAL uses an assisted assembly algorithm that borrows from ALLPATHS.</description>
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  <url>http://www.broadinstitute.org/crd/wiki/index.php/VAAL_Main_Page</url>
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  <description>VAAL is a variant ascertainment algorithm that can be used to detect SNPs, indels, and more complex
genetic variants. On bacterial data sets, it achievies very high sensitivity, and near perfect
specificity. VAAL can be used to compare reads from one strain to a reference sequence from another
strain. It can also be used to compare reads from two strains to each other, using a third strain
to determine homology. For example, we have used VAAL to find a single mutation responsible for
bacterial resistance: the output of the program was that single mutation and no others.
VAAL uses an assisted assembly algorithm that borrows from ALLPATHS.</description>
  <packager/>
  <url>http://www.broadinstitute.org/crd/wiki/index.php/VAAL_Main_Page</url>
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    <file>/usr/bin/VAALCompareCompound</file>
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  <description>Velvet is a set of algorithms manipulating de Bruijn graphs for genomic Sequence assembly.
It was designed for short read sequencing technologies, such as Solexa or 454 Sequencing
and was developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute.

The tool takes in short read sequences, removes errors then produces high quality unique
contigs. It then uses paired-end read and long read information, when available, to retrieve
the repeated areas between contigs.</description>
  <packager/>
  <url>http://www.ebi.ac.uk/~zerbino/velvet/</url>
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It was designed for short read sequencing technologies, such as Solexa or 454 Sequencing
and was developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute.

The tool takes in short read sequences, removes errors then produces high quality unique
contigs. It then uses paired-end read and long read information, when available, to retrieve
the repeated areas between contigs.</description>
  <packager/>
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  <summary>Sequence assembler for very short reads</summary>
  <description>Velvet is a set of algorithms manipulating de Bruijn graphs for genomic Sequence assembly.
It was designed for short read sequencing technologies, such as Solexa or 454 Sequencing
and was developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute.

The tool takes in short read sequences, removes errors then produces high quality unique
contigs. It then uses paired-end read and long read information, when available, to retrieve
the repeated areas between contigs.</description>
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Debug information is useful when developing applications that use this
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  <description>This package provides debug information for package velvet.
Debug information is useful when developing applications that use this
package or when debugging this package.</description>
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