Gene Annotation Template
Gene Annotation Log - Template
Basic Information:
DNA Coordinates:
DNA Sequence (FASTA format):
Protein Sequence (FASTA format):
Isoelectric Point:
Similarity Data (Sequence-Based):
BLAST Data:
- Gene Product Name:
- Top hit – organism:
- Length, Score, E-value, Identity, Positives and Gaps
NCBI Statistics
- Alignment of Top Hit and Query Sequence
Alignment Scoring
CDD: Conserved Domains Database
- Significant COG Hits:
Definition of COG
- Names of COGs:
- Score:
- E-value:
CDD website
PDB: Protein Data Bank
- Significant Structure Hits:
This database provides information about the structures of proteins in addition to performing a BLAST alignment.
o Length
o Score
o E-value
o Identities
o Positives
o Gaps
o Alignment
PDB website
T-Coffee:
- Multi-Sequence Alignment
T-coffee Website
Cellular Localization Data:
TMHMM:
- Number of Predicted TMH’s
- Transmembrane Topology graph and comment
SignalP:
- Signal Peptide Probability
- Signal Peptide Graph
PSORT:
- Cytoplasmic Score:
- Cytoplasmic Membrane Score:
- Periplasmic Score:
- Outer Membrane Score:
- Extracellular Score:
- Final Prediction for Protein Location (of the above listed):
Phobius:
- Enter Graph:
Final Hypothesis: Where do you expect to find this protein?
Alternative Open Reading Frames:
Proposed DNA Coordinates:
Reasoning:
Structure-Based Evidence of Function:
Pfam-A:
- Significant Matches:
- Pfam Name:
- Pairwise Alignment:
- HMM logo:
- Key Functional Residues:
PDB:
- Significant Structure Hits:
o Length
o Score
o E-value
o Identities
o Positives
o Gaps
- Alignment:
Pathways:
KEGG - Map:
EcoCyc – Pathway:
E.C. Number:
Duplication and Degradation:
Paralog:
- Length
- Score
- E-value
- Identity
- Positives
- Gaps
Alignment of Top Hit and Query Sequence:
Evidence of Horizontal Gene Transfer:
Phylogenetic Tree Diagram:
Gene Context:
- Ortholog Neighborhood Region of Organism:
- Examples of similarities or Differences:
- Comment:
Chromosome Viewer GC Heat Map:
- Characteristic GC% of genome:
- Average GC% of gene:
RNA (Rfam):
RNA Family:
Bits Score:
