PhageFlowan LW Sciences tool
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Student guide

SEA-PHAGES Annotation Walk-through

A compact classroom guide for staying oriented while moving from a FASTA file to a reviewable draft annotation. It supports the official guide and instructor review; it does not replace either one.

1

Start With The FASTA

Confirm there is one sequence record, the sequence uses DNA bases, and the phage name/length are recorded.

  • >PhageName
  • ATGCGT...
  • Watch for N bases, fragments, or a header that says complete genome when the sequence is short.
2

Whole-Genome Context

Use genome-level comparison to understand what kind of phage this probably is.

  • Record top related phages.
  • Record cluster/subcluster hints.
  • Do not assign gene functions from this step alone.
3

Draft Gene Calls

Gene callers propose where genes might be. Treat them as suggestions, not final answers.

  • Compare GeneMark/Glimmer/PHEONA evidence.
  • Check coding potential.
  • Flag short genes, large gaps, and big overlaps.
4

Check Starts And Stops

For each gene, compare possible starts and choose the one best supported by multiple evidence types.

  • Do not pick the longest ORF just because it is longest.
  • Prefer good coding potential and reasonable ribosome binding support.
5

Predict Function

Use protein-level evidence to decide what each gene probably does.

  • Use BLASTp, conserved domains, Pfam/HMMER, HHpred later, and related phage annotations.
  • Weak evidence means hypothetical protein.
6

Instructor Review

Review questionable calls before anything official. The goal is a well-supported draft, not blind automation.

  • Check tRNAs/tmRNAs, odd gaps, repeated functions, and genes whose function conflicts with context.
  • Keep notes explaining accepted or changed calls.

Evidence strength

Use the strongest specific evidence you have.

StrongMultiple close BLASTp hits agree, conserved domains support the same function, and related phage annotations match.
MediumOne decent hit, a domain hit with unclear exact function, or related phages that are similar but not very close.
WeakPoor E-value, vague hit names, conflicting evidence, or no conserved domain. Use conservative wording.
NoneUse hypothetical protein and leave the evidence visible for review.

What PhageFlow Should Do

  • Validate the FASTA.
  • Find draft genes.
  • Find likely relatives.
  • Gather evidence for each gene.
  • Flag questionable calls.
  • Show everything in one review screen.

What It Should Not Do

  • Submit final annotations automatically.
  • Hide evidence from students.
  • Replace instructor review.
  • Treat baseline ORFs as final gene calls.