Difference between revisions of "BIO Reference data"

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Reference data
 
Reference data
 
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__NOTOC__
  
 
<section begin=contents_summary />
 
<section begin=contents_summary />
 
Annotated links to reference data for Bioinformatics course assignments.
 
Annotated links to reference data for Bioinformatics course assignments.
 
<section end=contents_summary />
 
<section end=contents_summary />
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====Species====
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;[[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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====Sequences and Annotations====
  
 
;[[Reference annotation yeast Mbp1]]
 
;[[Reference annotation yeast Mbp1]]
 
<div style="padding-left:20px;">{{#lst:Reference annotation yeast Mbp1|contents_summary}}</div>
 
<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 species for fungi]]
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;[[Reference Mbp1 orthologues (all fungi)]]
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:{{#lst:Reference species for fungi|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 proteins (reference species)]]
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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 APSES domain sequences (reference species)]]
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;[[Reference APSES domains (reference species)]]
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:{{#lst:Reference APSES domain sequences (reference species)|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 domains (MUSCLE, reference species)]]
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;[[Reference APSES domains (yeast)]]
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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 APSES domains (yeast)|contents_summary}}</div>
  
  
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;[[Reference tree for APSES domains]]
 
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:{{#lst:Reference tree for APSES domains|contents_summary}}
 
  
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====Alignments====
  
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;[[Reference APSES domains (yeast)]]
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;[[Reference alignment for Mbp1 orthologues (MUSCLE)]]
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:{{#lst:Reference APSES domains (yeast)|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" />
  
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;[[Reference list of APSES protein sequences]]
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;[[Reference alignment for Mbp1 orthologues (T-COFFEE)]]
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:{{#lst:Reference list of APSES protein sequences|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" />
  
 
;[[Reference alignment for APSES domain proteins (PSI-BLAST)]]
 
;[[Reference alignment for APSES domain proteins (PSI-BLAST)]]
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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 alignment for APSES domain proteins (PSI-BLAST)|contents_summary}}</div>
  
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<hr width=30% align="left" />
  
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;[[Reference alignment for Mbp1 orthologues (MUSCLE)]]
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;[[Reference alignment for APSES domains (MUSCLE, reference species)]]
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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 APSES domains (MUSCLE, reference species)|contents_summary}}</div>
  
  
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;[[Reference alignment for Mbp1 orthologues (T-COFFEE)]]
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====Trees====
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:{{#lst:Reference alignment for Mbp1 orthologues (T-COFFEE)|contents_summary}}
 
  
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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>
 
&nbsp;
 
&nbsp;
 
[[Category:Bioinformatics]]
 
[[Category:Bioinformatics]]
  
 
</div>
 
</div>

Revision as of 01:15, 2 December 2014

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 APSES domain proteins (PSI-BLAST)
Reference alignment for APSES domains (MUSCLE, reference species)


Trees

Reference tree for APSES domains

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

 

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