BIO Reference data

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.

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Reference Mbp1 orthologues (all fungi)

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

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Reference APSES proteins (reference species)

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

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Reference APSES domains (reference species)

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

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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.

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Reference alignment for Mbp1 orthologues (T-COFFEE)

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

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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.

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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.