Difference between revisions of "Gene Annotation Template"
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'''Cellular Localization Data:'''<br> | '''Cellular Localization Data:'''<br> | ||
<br> | <br> | ||
− | TMHMM: | + | TMHMM:<br> |
− | - Number of Predicted TMH’s | + | - Number of Predicted TMH’s<br> |
− | - Transmembrane Topology graph and comment | + | - Transmembrane Topology graph and comment<br> |
− | SignalP: | + | <br> |
− | - Signal Peptide Probability | + | SignalP:<br> |
− | - Signal Peptide Graph | + | - Signal Peptide Probability <br> |
− | PSORT: | + | - Signal Peptide Graph<br> |
− | - Cytoplasmic Score: | + | <br> |
− | - Cytoplasmic Membrane Score | + | PSORT:<br> |
− | - Periplasmic Score: | + | - Cytoplasmic Score:<br> |
− | - Outer Membrane Score: | + | - Cytoplasmic Membrane Score:<br> |
− | - Extracellular Score: | + | - Periplasmic Score:<br> |
− | - Final Prediction for Protein Location (of the above listed): | + | - Outer Membrane Score:<br> |
− | Phobius: | + | - Extracellular Score:<br> |
− | - Enter Graph: | + | - Final Prediction for Protein Location (of the above listed):<br> |
− | Final Hypothesis: Where do you expect to find this protein? | + | <br> |
− | Alternative Open Reading Frames: | + | Phobius:<br> |
− | Proposed DNA Coordinates: | + | - Enter Graph:<br> |
− | Reasoning: | + | <br> |
− | Structure-Based Evidence of Function: | + | Final Hypothesis: Where do you expect to find this protein?<br> |
− | Pfam-A: | + | <br> |
− | - Significant Matches: | + | |
− | - Pfam Name: | + | ---- |
− | - Pairwise Alignment: | + | |
− | - HMM logo: | + | <br> |
− | - Key Functional Residues: | + | |
− | PDB: | + | '''Alternative Open Reading Frames:'''<br> |
− | - Significant Structure Hits: | + | <br> |
− | o Length | + | Proposed DNA Coordinates:<br> |
− | o Score | + | <br> |
− | o E-value | + | Reasoning:<br> |
− | o Identities | + | <br> |
− | o Positives | + | |
− | o Gaps | + | ---- |
− | - Alignment: | + | |
− | Pathways: | + | <br> |
− | KEGG – Map: | + | '''Structure-Based Evidence of Function:'''<br> |
− | EcoCyc – Pathway: | + | <br> |
− | E.C. Number: | + | Pfam-A:<br> |
− | Duplication and Degradation: | + | - Significant Matches:<br> |
− | Paralog: | + | - Pfam Name:<br> |
− | - Length | + | - Pairwise Alignment:<br> |
− | - Score | + | - HMM logo:<br> |
− | - E-value | + | - Key Functional Residues:<br> |
− | - Identity | + | <br> |
− | - Positives | + | PDB:<br> |
− | - Gaps | + | - Significant Structure Hits:<br> |
− | Alignment of Top Hit and Query Sequence: | + | o Length<br> |
− | Evidence of Horizontal Gene Transfer: | + | o Score<br> |
− | Phylogenetic Tree Diagram: | + | o E-value<br> |
− | Gene Context: | + | o Identities<br> |
− | - Ortholog Neighborhood Region of Organism: | + | o Positives<br> |
− | - Examples of similarities or Differences: | + | o Gaps<br> |
− | - Comment: | + | - Alignment:<br> |
− | Chromosome Viewer GC Heat Map: | + | <br> |
− | - Characteristic GC% of genome: | + | |
− | - Average GC% of gene: | + | ---- |
− | RNA (Rfam): | + | |
− | RNA Family: | + | <br> |
− | Bits Score: | + | '''Pathways:'''<br> |
− | Alignment: | + | <br> |
+ | KEGG – Map:<br> | ||
+ | EcoCyc – Pathway:<br> | ||
+ | E.C. Number: <br> | ||
+ | <br> | ||
+ | |||
+ | ---- | ||
+ | |||
+ | <br> | ||
+ | '''Duplication and Degradation:'''<br> | ||
+ | <br> | ||
+ | Paralog:<br> | ||
+ | - Length<br> | ||
+ | - Score<br> | ||
+ | - E-value<br> | ||
+ | - Identity<br> | ||
+ | - Positives<br> | ||
+ | - Gaps<br> | ||
+ | <br> | ||
+ | Alignment of Top Hit and Query Sequence:<br> | ||
+ | <br> | ||
+ | |||
+ | ---- | ||
+ | |||
+ | <br> | ||
+ | |||
+ | '''Evidence of Horizontal Gene Transfer:'''<br> | ||
+ | <br> | ||
+ | Phylogenetic Tree Diagram:<br> | ||
+ | <br> | ||
+ | Gene Context:<br> | ||
+ | - Ortholog Neighborhood Region of Organism:<br> | ||
+ | - Examples of similarities or Differences:<br> | ||
+ | - Comment:<br> | ||
+ | <br> | ||
+ | Chromosome Viewer GC Heat Map:<br> | ||
+ | - Characteristic GC% of genome:<br> | ||
+ | - Average GC% of gene:<br> | ||
+ | <br> | ||
+ | |||
+ | ---- | ||
+ | |||
+ | <br> | ||
+ | '''RNA (Rfam):'''<br> | ||
+ | <br> | ||
+ | RNA Family:<br> | ||
+ | Bits Score:<br> | ||
+ | Alignment:<br> |
Revision as of 02:15, 4 September 2008
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
- Alignment of Top Hit and Query Sequence
CDD:
- Significant COG Hits:
- Names of COGs:
- Score:
- E-value:
PDB:
- Significant Structure Hits:
o Length
o Score
o E-value
o Identities
o Positives
o Gaps
o Alignment
T-Coffee:
- Multi-Sequence Alignment
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: