Comments (5)
In the Retroviridae family this problem is very prevalent
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Examples:
-
Cluster 2: In HIV-1 genome
NC_001802
,Gag-Pol
(335 to 1637) andPr55(Gag)
(335 to 1838) overlap. Same thing happen on Mouse mammary tumor virusNC_001503
, wherePr160
(gene = gag-pol-pro) andPr77
(gene = gag) overlap. -
Cluster 1: Snakehead retrovirus
NC_001724
is an interesting case where a lot of proteins are hypothetical. For examplehypothetical protein
from9345 to 9535
overlaps withhypothetical protein
from9345 to 9357
. When exploring the genome, there are 17 hypothetical proteins, several of which share similar ORFS. -
Cluster 3: In Moloney murine sarcoma virus
NC_001502
, the pol polyprotein fragment coordinates are:2485..2928; 2927..3388
. We are treating every segment of a protein as an individual unit; therefore this protein seems to be overlapping to itself (this is probably a Ribosomal shift on the reading frame). -
Cluster 5: In Equine infectious anemia virus
NC_001450
there is only one hypothetical protein with coordinates7295..7951
that apparently has a self edge. This one I don't understand why is being created.
Overall, the self-edge count for overlapping genes in the Retroviridae family is the following:
Cluster: 1, Numer of self edges: 29
Cluster: 2, Numer of self edges: 65
Cluster: 3, Numer of self edges: 1
Cluster: 4, Numer of self edges: 34
Cluster: 5, Numer of self edges: 1
Cluster: 6, Numer of self edges: 16
From exploring the situation, it seems that self edges are formed when two proteins of the same genome are very similar to each other, therefore classified on the same cluster. However, we need to fix the current implementation where two parts of the same protein are being interpreted as individual units.
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Word Clouds for Retroviridae family
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Post cluster result
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Related Issues (20)
- Overlap lengths not being computed correctly
- find_ovrfs.py: error at calculating total overlap HOT 1
- HTTP Error HOT 4
- Plotting information HOT 2
- Adjust for non-independence of virus genomes
- Developing new visualization method HOT 17
- k-mer distance matrix HOT 6
- Apply clustering method to distance matrix from #12 HOT 14
- Create one plot for at least one family on every Baltimore Classification HOT 5
- Summary statistics for weighted graphs HOT 8
- Bigger picture: Mononegavirales HOT 1
- Re-analysing all NCBI database HOT 2
- Get proportion of overlapping edges over total edges
- Improving adjacency graphs HOT 25
- Paper HOT 2
- Retrovirus clustering HOT 3
- Wrong labels on JS graph HOT 1
- Error on overlap calculation HOT 8
- Visualization bugs
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