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[gofriends] New subcodes of ISS are now available
Gwinn Giglio, Michelle
mgiglio at som.umaryland.edu
Tue Apr 1 14:18:23 PDT 2008
Hello GO Friends,
As announced in the February 2008 GO newsletter, the GO Consortium has added
three new subcodes for the ISS (Inferred from Sequence or Structural
Similarity) evidence code. These go into effect today. These codes have
been created to clarify the type of sequence-based methods used as evidence
in making annotations. The new codes are: Inferred from Sequence Alignment
(ISA), Inferred from Sequence Orthology (ISO), and Inferred from Sequence
Detailed documentation describing each of these codes is now available on
the GO Evidence Code page: http://www.geneontology.org/GO.evidence.shtml
Some brief descriptions of the new codes:
ISA should be used when an annotation is based on pairwise or multiple
alignments of the query protein with experimentally characterized proteins.
Examples of tools that produce these types of alignments are BLAST, MUSCLE,
ISO should be used when a protein is determined to be orthologous with an
experimentally characterized protein from another species. Orthologous genes
share a common ancestor and have arisen due to a speciation event. Orthologs
are determined from phylogenetic analysis using algorithms such as maximum
likelihood or nearest neighbor joining.
ISM indicates use of a statistical modeling tool to determine a protein¹s
membership in a particular functional family, or to predict the presence of
a particular sequence domain or structure. Examples of ISM evidence types
are Hidden Markov Models (HMMs), tRNAscan, and transmembrane-HMM (TMHMM).
Many thanks to everyone on the Evidence Committee for their work on writing
the new documentation and getting it up onto the web page.
Please let us know if you have any questions.
Michelle (and the rest of the Evidence Committee)
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