Difference between revisions of "BIO Reference data"

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Reference data
 
Reference data
 
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;[[Reference annotation yeast Mbp1]]
 
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:{{#lst:Reference annotation yeast Mbp1|contents_summary}}
 
  
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====Species====
  
 
;[[Reference species for fungi]]
 
;[[Reference species for fungi]]
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<div style="padding-left:20px">{{#lst:Reference species for fungi|contents_summary}}</div>
  
  
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;[[Reference APSES domain sequences (reference species)]]
 
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:{{#lst:Reference APSES domain sequences (reference species)|contents_summary}}
 
  
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====Sequences and Annotations====
  
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;[[Reference alignment for APSES domains (MUSCLE, reference species)]]
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;[[Reference annotation yeast Mbp1]]
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:{{#lst:Reference alignment for APSES domains (MUSCLE, reference species)|contents_summary}}
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<div style="padding-left:20px;">{{#lst:Reference annotation yeast Mbp1|contents_summary}}</div>
  
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<hr width=30% align="left" />
  
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;[[Reference tree for APSES domains]]
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;[[Reference Mbp1 orthologues (all fungi)]]
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:{{#lst:Reference tree for APSES domains|contents_summary}}
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<div style="padding-left:20px;">{{#lst:Reference Mbp1 orthologues (all fungi)|contents_summary}}</div>
  
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<hr width=30% align="left" />
  
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;[[Reference APSES domains (yeast)]]
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;[[Reference APSES proteins (reference species)]]
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:{{#lst:Reference APSES domains (yeast)|contents_summary}}
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<div style="padding-left:20px;">{{#lst:Reference APSES proteins (reference species)|contents_summary}}</div>
  
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<hr width=30% align="left" />
  
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;[[Reference list of APSES protein sequences]]
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;[[Reference APSES domains (reference species)]]
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:{{#lst:Reference list of APSES protein sequences|contents_summary}}
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<div style="padding-left:20px;">{{#lst:Reference APSES domains (reference species)|contents_summary}}</div>
  
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<hr width=30% align="left" />
  
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;[[Reference alignment for APSES domain proteins (PSI-BLAST)]]
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;[[Reference APSES domains (yeast)]]
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:{{#lst:Reference alignment for APSES domain proteins (PSI-BLAST)|contents_summary}}
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<div style="padding-left:20px;">{{#lst:Reference APSES domains (yeast)|contents_summary}}</div>
  
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====Alignments====
  
 
;[[Reference alignment for Mbp1 orthologues (MUSCLE)]]
 
;[[Reference alignment for Mbp1 orthologues (MUSCLE)]]
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:{{#lst:Reference alignment for Mbp1 orthologues (MUSCLE)|contents_summary}}
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<div style="padding-left:20px;">{{#lst:Reference alignment for Mbp1 orthologues (MUSCLE)|contents_summary}}</div>
  
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<hr width=30% align="left" />
  
 
;[[Reference alignment for Mbp1 orthologues (T-COFFEE)]]
 
;[[Reference alignment for Mbp1 orthologues (T-COFFEE)]]
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:{{#lst:Reference alignment for Mbp1 orthologues (T-COFFEE)|contents_summary}}
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<div style="padding-left:20px;">{{#lst:Reference alignment for Mbp1 orthologues (T-COFFEE)|contents_summary}}</div>
  
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<hr width=30% align="left" />
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;[[Reference alignment for KilA-N domain proteins (PSI-BLAST)]]
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<div style="padding-left:20px;">{{#lst:Reference alignment for KilA-N domain proteins (PSI-BLAST)|contents_summary}}</div>
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<hr width=30% align="left" />
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;[[Reference alignment for KilA-N domains (MUSCLE, reference species)]]
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<div style="padding-left:20px;">{{#lst:Reference alignment for KilA-N domains (MUSCLE, reference species)|contents_summary}}</div>
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====Trees====
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;[[Reference tree for APSES domains]]
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<div style="padding-left:20px;">{{#lst:Reference tree for APSES domains|contents_summary}}</div>
 
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[[Category:Bioinformatics]]
 
[[Category:Bioinformatics]]
  
 
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Latest revision as of 11:14, 26 October 2015

Reference data


Annotated links to reference data for Bioinformatics course assignments.


Species

Reference species for fungi

Explanation and definition for the "reference species" we use for the course.


Sequences and Annotations

Reference annotation yeast Mbp1

A reference annotation of the Saccharomyces cerevisiae Mbp1 protein sequence that integrates annotation sources we encounter throughout the course.

Reference Mbp1 orthologues (all fungi)

Sequences for yeast Mbp1 orthologues (by RBM) in (all) genome sequenced fungi - multi FASTA format.

Reference APSES proteins (reference species)

APSES domain proteins in ten fungal reference species. PSI-BLAST search.

Reference APSES domains (reference species)

Sequences of APSES domains in the fungal reference species - domain definition, PSI-BLAST search, and header editing.

Reference APSES domains (yeast)

All APSES domains from APSES domain proteins in saccharomyces cerevisiae - annotated.

Alignments

Reference alignment for Mbp1 orthologues (MUSCLE)

A multiple sequence alignment for orthologues (by RBM) to saccharomyces cerevisiae Mbp1 - computed with MUSCLE.

Reference alignment for Mbp1 orthologues (T-COFFEE)

A multiple sequence alignment for orthologues (by RBM) to saccharomyces cerevisiae Mbp1 - computed with T-COFFEE.

Reference alignment for KilA-N domain proteins (PSI-BLAST)

A multiple sequence alignment of all KilA-N domains found in the reference fungi - derived from a PSI-BLAST search.

Reference alignment for KilA-N domains (MUSCLE, reference species)

Alignment of KilA-N domains in selected genome sequenced fungi, generated with the MUSCLE webserver.

Trees

Reference tree for APSES domains

A phylogentic tree for all APSES domains found in the reference fungi.

 

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