Conversion events in gene clusters
<p>Abstract</p> <p>Background</p> <p>Gene clusters containing multiple similar genomic regions in close proximity are of great interest for biomedical studies because of their associations with inherited diseases. However, such regions are difficult to analyze due to th...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2011-07-01
|
| Series: | BMC Evolutionary Biology |
| Online Access: | http://www.biomedcentral.com/1471-2148/11/226 |
| _version_ | 1818567006921687040 |
|---|---|
| author | Hardison Ross C Zhang Louxin Hoffmann Federico Kim Hie Zhang Yu Riemer Cathy Hsu Chih-Hao Song Giltae Green Eric D Miller Webb |
| author_facet | Hardison Ross C Zhang Louxin Hoffmann Federico Kim Hie Zhang Yu Riemer Cathy Hsu Chih-Hao Song Giltae Green Eric D Miller Webb |
| author_sort | Hardison Ross C |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Gene clusters containing multiple similar genomic regions in close proximity are of great interest for biomedical studies because of their associations with inherited diseases. However, such regions are difficult to analyze due to their structural complexity and their complicated evolutionary histories, reflecting a variety of large-scale mutational events. In particular, conversion events can mislead inferences about the relationships among these regions, as traced by traditional methods such as construction of phylogenetic trees or multi-species alignments.</p> <p>Results</p> <p>To correct the distorted information generated by such methods, we have developed an automated pipeline called CHAP (Cluster History Analysis Package) for detecting conversion events. We used this pipeline to analyze the conversion events that affected two well-studied gene clusters (α-globin and β-globin) and three gene clusters for which comparative sequence data were generated from seven primate species: CCL (chemokine ligand), IFN (interferon), and CYP2abf (part of cytochrome P450 family 2). CHAP is freely available at <url>http://www.bx.psu.edu/miller_lab</url>.</p> <p>Conclusions</p> <p>These studies reveal the value of characterizing conversion events in the context of studying gene clusters in complex genomes.</p> |
| first_indexed | 2024-12-14T06:17:55Z |
| format | Article |
| id | doaj.art-fe6f86bee5104182bba3845edd3b0f04 |
| institution | Directory Open Access Journal |
| issn | 1471-2148 |
| language | English |
| last_indexed | 2024-12-14T06:17:55Z |
| publishDate | 2011-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Evolutionary Biology |
| spelling | doaj.art-fe6f86bee5104182bba3845edd3b0f042022-12-21T23:13:59ZengBMCBMC Evolutionary Biology1471-21482011-07-0111122610.1186/1471-2148-11-226Conversion events in gene clustersHardison Ross CZhang LouxinHoffmann FedericoKim HieZhang YuRiemer CathyHsu Chih-HaoSong GiltaeGreen Eric DMiller Webb<p>Abstract</p> <p>Background</p> <p>Gene clusters containing multiple similar genomic regions in close proximity are of great interest for biomedical studies because of their associations with inherited diseases. However, such regions are difficult to analyze due to their structural complexity and their complicated evolutionary histories, reflecting a variety of large-scale mutational events. In particular, conversion events can mislead inferences about the relationships among these regions, as traced by traditional methods such as construction of phylogenetic trees or multi-species alignments.</p> <p>Results</p> <p>To correct the distorted information generated by such methods, we have developed an automated pipeline called CHAP (Cluster History Analysis Package) for detecting conversion events. We used this pipeline to analyze the conversion events that affected two well-studied gene clusters (α-globin and β-globin) and three gene clusters for which comparative sequence data were generated from seven primate species: CCL (chemokine ligand), IFN (interferon), and CYP2abf (part of cytochrome P450 family 2). CHAP is freely available at <url>http://www.bx.psu.edu/miller_lab</url>.</p> <p>Conclusions</p> <p>These studies reveal the value of characterizing conversion events in the context of studying gene clusters in complex genomes.</p>http://www.biomedcentral.com/1471-2148/11/226 |
| spellingShingle | Hardison Ross C Zhang Louxin Hoffmann Federico Kim Hie Zhang Yu Riemer Cathy Hsu Chih-Hao Song Giltae Green Eric D Miller Webb Conversion events in gene clusters BMC Evolutionary Biology |
| title | Conversion events in gene clusters |
| title_full | Conversion events in gene clusters |
| title_fullStr | Conversion events in gene clusters |
| title_full_unstemmed | Conversion events in gene clusters |
| title_short | Conversion events in gene clusters |
| title_sort | conversion events in gene clusters |
| url | http://www.biomedcentral.com/1471-2148/11/226 |
| work_keys_str_mv | AT hardisonrossc conversioneventsingeneclusters AT zhanglouxin conversioneventsingeneclusters AT hoffmannfederico conversioneventsingeneclusters AT kimhie conversioneventsingeneclusters AT zhangyu conversioneventsingeneclusters AT riemercathy conversioneventsingeneclusters AT hsuchihhao conversioneventsingeneclusters AT songgiltae conversioneventsingeneclusters AT greenericd conversioneventsingeneclusters AT millerwebb conversioneventsingeneclusters |