ArticleAlgorithms for molecular biology : AMB2009
CHSMiner: a GUI tool to identify chromosomal homologous segments.
Article in Algorithms for molecular biology : AMB, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 12 citations in OpenAlex.
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- Genome sequence of Anopheles sinensis provides insight into genetics basis of mosquito competence for malaria parasites.BMC genomics · 2014Article
- The evolutionary portrait of metazoan NAD salvage.PloS one · 2013Article
- Genome sequences of wild and domestic bactrian camels.Nature communications · 2012Article
- Whole-genome duplications spurred the functional diversification of the globin gene superfamily in vertebrates.Molecular biology and evolution · 2012Article
- Molecular phylogeny and functional genomics of beta-galactoside alpha2,6-sialyltransferases that explain ubiquitous expression of st6gal1 gene in amniotes.The Journal of biological chemistry · 2010Article
- Comparing the retention mechanisms of tandem duplicates and retrogenes in human and mouse genomes.Genetics, selection, evolution : GSE · 2010Article
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe identification of chromosomal homologous segments (CHS) within and between genomes is essential for comparative genomics. Various processes including insertion/deletion and inversion could cause the degeneration of CHSs.
resultsHere we present a Java software CHSMiner that detects CHSs based on shared gene content alone. It implements fast greedy search algorithm and rigorous statistical validation, and its friendly graphical interface allows interactive visualization of the results. We tested the software on both simulated and biological realistic data and compared its performance with similar existing software and data source.
conclusionCHSMiner is characterized by its integrated workflow, fast speed and convenient usage. It will be useful for both experimentalists and bioinformaticians interested in the structure and evolution of genomes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.