It is now the 1st OPEN Period for CACAO Fall 2017! It will end on Sunday September 24, 2017 at 11:59 pm CDT
This is your chance to make annotations OR challenge other team's annotations. You may also DEFEND or suggest improvements to your own annotations IF they have been challenged. Please note, although we ENCOURAGE challenges, an excess of identical challenges that do not appear to be applicable to the annotation or well thought out will be considered spam and ignored.

Have any questions? Please email us at ecoliwiki@gmail.com

GO REF:BLAST

From GONUTS
Jump to: navigation, search

Definition

BLAST[1] is a tool for searching nucleotide or amino acid databases using nucleotide or amino acid sequences as a query. BLAST comes in different flavors (e.g. BLASTP, tBLASTX), allowing us to search different databases (nucleotide or amino acid) using different query types (amino acid or protein). BLAST is available as a web service on most sequence repositories, including NCBI and EBI.

Usage

In the context of Gene Ontology annotation, BLAST is used primarily to identify sequences similar to the sequence of interest (the query) we wish to annotate. Upon validating that the identified database sequence in the database meets the provided criteria to establish homology between the two sequences, experimental code-based annotations on the database sequence can be transferred to the sequence of interest (our query) citing the CACAO GO_REF as a source and using evidence codes ISS, ISA or ISO.

Criteria

Several criteria are used to inspect and validate that alignments returned by BLAST are indicative of sequence homology and can be used to transfer existing GO annotations for a database hit to our sequence of interest. These criteria apply to overall BLAST results statistics (e.g. e-value), assessment of the quality and extension of the generated alignments and evaluation of the transferability of an existing annotation to the biological context of the sequence of interest. The database sequence used in the preexisting GO annotation must be referenced in the WITH field using an appropriate identifier.


The following links define the criteria to be used for transferring annotations under evidence codes ISS, ISA and ISO using different BLAST flavors:

References

  1. Altschul, SF et al. (1990) Basic local alignment search tool. J. Mol. Biol. 215 403-10 PubMed GONUTS page