Retrieving sequences of enzymes experimentally characterized but erroneously annotated : the case of the putrescine carbamoyltransferase
<p>Abstract</p> <p>Background</p> <p>Annotating genomes remains an hazardous task. Mistakes or gaps in such a complex process may occur when relevant knowledge is ignored, whether lost, forgotten or overlooked. This paper exemplifies an approach which could help to ress...
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| Format: | Article |
| Language: | English |
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BMC
2004-08-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/5/52 |
| _version_ | 1818494726028918784 |
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| author | Glansdorff Nicolas Xu Ying Naumoff Daniil G Labedan Bernard |
| author_facet | Glansdorff Nicolas Xu Ying Naumoff Daniil G Labedan Bernard |
| author_sort | Glansdorff Nicolas |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Annotating genomes remains an hazardous task. Mistakes or gaps in such a complex process may occur when relevant knowledge is ignored, whether lost, forgotten or overlooked. This paper exemplifies an approach which could help to ressucitate such meaningful data.</p> <p>Results</p> <p>We show that a set of closely related sequences which have been annotated as ornithine carbamoyltransferases are actually putrescine carbamoyltransferases. This demonstration is based on the following points : (i) use of enzymatic data which had been overlooked, (ii) rediscovery of a short NH<sub>2</sub>-terminal sequence allowing to reannotate a wrongly annotated ornithine carbamoyltransferase as a putrescine carbamoyltransferase, (iii) identification of conserved motifs allowing to distinguish unambiguously between the two kinds of carbamoyltransferases, and (iv) comparative study of the gene context of these different sequences.</p> <p>Conclusions</p> <p>We explain why this specific case of misannotation had not yet been described and draw attention to the fact that analogous instances must be rather frequent. We urge to be especially cautious when high sequence similarity is coupled with an apparent lack of biochemical information. Moreover, from the point of view of genome annotation, proteins which have been studied experimentally but are not correlated with sequence data in current databases qualify as "orphans", just as unassigned genomic open reading frames do. The strategy we used in this paper to bridge such gaps in knowledge could work whenever it is possible to collect a body of facts about experimental data, homology, unnoticed sequence data, and accurate informations about gene context.</p> |
| first_indexed | 2024-12-10T18:10:18Z |
| format | Article |
| id | doaj.art-f0381aacaff341c0a6132d6f31b4bd4d |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-10T18:10:18Z |
| publishDate | 2004-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-f0381aacaff341c0a6132d6f31b4bd4d2022-12-22T01:38:28ZengBMCBMC Genomics1471-21642004-08-01515210.1186/1471-2164-5-52Retrieving sequences of enzymes experimentally characterized but erroneously annotated : the case of the putrescine carbamoyltransferaseGlansdorff NicolasXu YingNaumoff Daniil GLabedan Bernard<p>Abstract</p> <p>Background</p> <p>Annotating genomes remains an hazardous task. Mistakes or gaps in such a complex process may occur when relevant knowledge is ignored, whether lost, forgotten or overlooked. This paper exemplifies an approach which could help to ressucitate such meaningful data.</p> <p>Results</p> <p>We show that a set of closely related sequences which have been annotated as ornithine carbamoyltransferases are actually putrescine carbamoyltransferases. This demonstration is based on the following points : (i) use of enzymatic data which had been overlooked, (ii) rediscovery of a short NH<sub>2</sub>-terminal sequence allowing to reannotate a wrongly annotated ornithine carbamoyltransferase as a putrescine carbamoyltransferase, (iii) identification of conserved motifs allowing to distinguish unambiguously between the two kinds of carbamoyltransferases, and (iv) comparative study of the gene context of these different sequences.</p> <p>Conclusions</p> <p>We explain why this specific case of misannotation had not yet been described and draw attention to the fact that analogous instances must be rather frequent. We urge to be especially cautious when high sequence similarity is coupled with an apparent lack of biochemical information. Moreover, from the point of view of genome annotation, proteins which have been studied experimentally but are not correlated with sequence data in current databases qualify as "orphans", just as unassigned genomic open reading frames do. The strategy we used in this paper to bridge such gaps in knowledge could work whenever it is possible to collect a body of facts about experimental data, homology, unnoticed sequence data, and accurate informations about gene context.</p>http://www.biomedcentral.com/1471-2164/5/52 |
| spellingShingle | Glansdorff Nicolas Xu Ying Naumoff Daniil G Labedan Bernard Retrieving sequences of enzymes experimentally characterized but erroneously annotated : the case of the putrescine carbamoyltransferase BMC Genomics |
| title | Retrieving sequences of enzymes experimentally characterized but erroneously annotated : the case of the putrescine carbamoyltransferase |
| title_full | Retrieving sequences of enzymes experimentally characterized but erroneously annotated : the case of the putrescine carbamoyltransferase |
| title_fullStr | Retrieving sequences of enzymes experimentally characterized but erroneously annotated : the case of the putrescine carbamoyltransferase |
| title_full_unstemmed | Retrieving sequences of enzymes experimentally characterized but erroneously annotated : the case of the putrescine carbamoyltransferase |
| title_short | Retrieving sequences of enzymes experimentally characterized but erroneously annotated : the case of the putrescine carbamoyltransferase |
| title_sort | retrieving sequences of enzymes experimentally characterized but erroneously annotated the case of the putrescine carbamoyltransferase |
| url | http://www.biomedcentral.com/1471-2164/5/52 |
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