BNFO 301 
Introduction to Bioinformatics
Topic: Annotation Checklist
Spring 2012 

Individual Responsibilities

  1. You've annotated all genes given to you for Pass 1
     
    1. See the link to Frederick, Maverick, or Pari (also available on the Genome Analysis page) for a list of what those genes are.
       
    2. See the suggestions on how to annotate the genes (also available on the course Calendar, March 19).
       
    3. At minimum, you have processed the following fields for each gene:
      • the Main Annotation field
      • Either the From Coordinate or To Coordinate field (the one corresponding to the start codon) but not both (don't change the stop codon)
      • the Operon Structure field
         
    4. You are encouraged to process the Membrane Spans and Signal Sequence fields as well.
       
    5. For any field you considered, you clicked the yellow box and made some entry in the Evidence field and Evidence Inferred From field, even if you made no change in the field you're annotating. This way, the world knows you were there and agree with the annotation (or not).
       
  2. You've considered all the genes given to you for Pass 2
     
    1. Note that all of your genes are next to each other.
       
    2. You've made sure all the genes have gone through Pass 1. If not, then you've bothered the person(s) responsible.
       
    3. You've considered each entry made in Pass 1. If there was sufficient evidence to justify the change (or non-change), then you've clicked the field and clicked Save. Your name will now be associated with the assertion.
       
    4. If you thought there was NOT sufficient evidence to justify the assertion of Pass 1 (e.g. you couldn't understand what it was saying) then you changed it to something you *could* live with. You might have contacted the original annotator to let him/her fix what you considered to be broken.
       
    5. You made sure that the annotations of all your genes are compatible with each other. This is particularly pertinent with regards to the Operon Structure field.
       
    6. You determined whether there are any alternate reading frames that do not appear in the current annotation that ought to be there. If you found one, you notified me or reported it to BioBIKE Central (by clicking Help then Report Problem).
       

Group Responsibilities

  1. The group has made sure that all genes have undergone Pass 1.
     
  2. The group has made sure that all genes have undergone Pass 2.
     
  3. When this has been done, the group has sent me the good news. All members of the group should get a copy of this message and agree with its content.