Reduction of redundancy in gene clusters

[lalintao]

The paper mentioned that redundant results of over 100 million gene clusters were removed, and then approximately 7,000 non-redundant gene clusters were obtained. However, no corresponding code was found in the paper. I would really like to discuss this with you. Is there still the script used for processing at that time, or could I ask you about the criteria you used to classify each type of gene cluster when removing redundancies?

[RuoshiZhang]

Hi! In the paper we removed redundant gene clusters for each query genome, by collapsing/aggregating overlapping query cluster positions regions that hit multiple target gene regions. Please refer to the bottom panel of figure 3a in the paper, where consecutive hit pairs (in pink shadings) were merged, and one of such areas was considered one non-redundant cluster.

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On Tue, 28 Oct 2025 at 09:25, lalintao ***@***.***> wrote: *lalintao* created an issue (soedinglab/spacedust#12) <#12> The paper mentioned that redundant results of over 100 million gene clusters were removed, and then approximately 7,000 non-redundant gene clusters were obtained. However, no corresponding code was found in the paper. I would really like to discuss this with you. Is there still the script used for processing at that time, or could I ask you about the criteria you used to classify each type of gene cluster when removing redundancies? — Reply to this email directly, view it on GitHub <#12>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHFHFQCD2FOIZNDWA2SJJRT3Z4R7RAVCNFSM6AAAAACKND6EPKVHI2DSMVQWIX3LMV43ASLTON2WKOZTGU3DAMZWGIYDONQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[lalintao]

Thank you very much for your response. Your reply has been immensely helpful to us. If I understand correctly, if I want to remove redundant gene clusters, I can treat each cluster in every query genome as a node, and ultimately merge them into a mapping relationship where one node corresponds to multiple nodes, thereby eliminating redundant gene clusters. If I replace the test genomes with other genomes, this data will change accordingly. Additionally, we would like to consult you in other issues regarding some problems we encountered while using spacedust in our work. We sincerely hope to receive your response, as it would be a great help to us. @RuoshiZhang