ANEXdb: An integrated annotation and expression database

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ANEXdb An integrated annotation and expression
database

• Oliver Couture

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Types of Annotation

• Sequence
• Function
• Roles of the conserved domains
• Expression
• Tissue, level

5 UTR
3 UTR
Protein coding conserved domains
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Sources of Annotation

• Sequence comparison
• Both sequence and function annotation can be
  predicted
• Quick and easy to do on genomic scale
• Experimental
• All three types of annotation can be verified
• Time intensive, few genomic scale methods
• Designing experiments usually requires good
  sequence annotation

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Getting Good Sequence for Annotation

• Sequence protein encoding regions
• EST sequencing of mRNA
• Most of the sequencing
• Cloning of mRNA
• Partial or full length
• Predicted from genomic sequence
• Need genome first

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Assembly of ESTs/Clones
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Post Assembly Annotation

• Homologue alignment
• BLAST to RefSeq RNA database at NCBI
• Use every available species
• Genomic alignment to certain species
• BLAST result and genomic alignment both map to
  the same place
• Sequence specific alignment
• Pfam

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Drawbacks

• BLAST is only a local alignment and uses
  heuristics
• Minor, but important, differences will be ignored
• Pfam only transfers information about part of
  sequence
• Use as a guide for the annotation of the gene

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Affymetrix Porcine GeneChip

• Current Affymetrix porcine array has only about
  15 of probe sets annotated with a gene name
• Most others are simply annotated as Transcribed
  Locus
• Some have additional information, but scarce
• Not very useful annotation on its own

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Contig Mapping
Affy target sequence
Contig Assembled sequence
RefSeq annotated sequence

• Fist align Affy target sequence to contig
• Contig already aligned to annotated RefSeq
  sequence
• Transfer annotation
• About 85 of Affy probe sets annotated this way

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Other Uses

• From assembly can predict putative SNPs
• Platform comparisons within species
• Map probe sets of each platform to a common
  contig
• Help validate the platforms
• Across species comparison
• Map elements to appropriate species and find
  homologous contig
• Measure difference/similarities between species