We encountered what appears to be an unexpected behavior while using the clustersearch module of spacedust. The target database comprises the query (Myxococcus xanthus DK 1622 RefSeq assembly: GCF_000012685.1) itself and another (Corallococcus coralloides strain Ccc1071, referred to as its strain identifier) genome. The latter contains the gene that clusters with a gene of interest (in the query).
The sequence headers for both the genomes were modified to a spacedust acceptable format. The Sequence Identifier of the gene of interest is NC_008095.1_3674_2394_4501281_4544105 (which is absent for query vs query). This is the output of spacedust clustersearch: result_minimal.tsv
Since the target database includes the query genome, we expected the query gene to also cluster with itself.
While using the clustersearch module of spacedust, the query gene of interest is clustered against a gene in the target genome but not against itself. What could be the reason behind this disparity? We tried repeating the clustersearch with different E-value flags, but this did not change the outcome.
Thank you for your time and assistance. We are also open to collaborating if this issue is of broader interest.
We encountered what appears to be an unexpected behavior while using the
clustersearchmodule ofspacedust. The target database comprises the query (Myxococcus xanthus DK 1622 RefSeq assembly: GCF_000012685.1) itself and another (Corallococcus coralloides strain Ccc1071, referred to as its strain identifier) genome. The latter contains the gene that clusters with a gene of interest (in the query).The sequence headers for both the genomes were modified to a
spacedustacceptable format. The Sequence Identifier of the gene of interest isNC_008095.1_3674_2394_4501281_4544105(which is absent for query vs query). This is the output ofspacedust clustersearch: result_minimal.tsvSince the target database includes the query genome, we expected the query gene to also cluster with itself.
While using the
clustersearchmodule ofspacedust, the query gene of interest is clustered against a gene in the target genome but not against itself. What could be the reason behind this disparity? We tried repeating theclustersearchwith different E-value flags, but this did not change the outcome.Thank you for your time and assistance. We are also open to collaborating if this issue is of broader interest.