Improved microbial gene identification with GLIMMER

Arthur L. Delcher; Douglas Harmon; Simon Kasif; Owen White; Steven L. Salzberg

doi:10.1093/nar/27.23.4636

Improved microbial gene identification with GLIMMER

Arthur L. Delcher, Douglas Harmon, Simon Kasif, Owen White, Steven L. Salzberg

Research output: Contribution to journal › Article › peer-review

1867 Scopus citations

Abstract

The GLIMMER system for microbial gene identification finds ~ 97-98% of all genes in a genome when compared with published annotation. This paper reports on two new results: (i) significant technical improvements to GLIMMER that improve its accuracy still further, and (ii) a comprehensive evaluation that demonstrates that the accuracy of the system is likely to be higher than previously recognized. A significant proportion of the genes missed by the system appear to be hypothetical proteins whose existence is only supported by the predictions of other programs. When the analysis is restricted to genes that have significant homology to genes in other organisms, GLIMMER misses < 1% of known genes.

Original language	English (US)
Pages (from-to)	4636-4641
Number of pages	6
Journal	Nucleic acids research
Volume	27
Issue number	23
DOIs	https://doi.org/10.1093/nar/27.23.4636
State	Published - Dec 1 1999
Externally published	Yes

ASJC Scopus subject areas

Genetics

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title = "Improved microbial gene identification with GLIMMER",

abstract = "The GLIMMER system for microbial gene identification finds ~ 97-98% of all genes in a genome when compared with published annotation. This paper reports on two new results: (i) significant technical improvements to GLIMMER that improve its accuracy still further, and (ii) a comprehensive evaluation that demonstrates that the accuracy of the system is likely to be higher than previously recognized. A significant proportion of the genes missed by the system appear to be hypothetical proteins whose existence is only supported by the predictions of other programs. When the analysis is restricted to genes that have significant homology to genes in other organisms, GLIMMER misses < 1% of known genes.",

author = "Delcher, {Arthur L.} and Douglas Harmon and Simon Kasif and Owen White and Salzberg, {Steven L.}",

note = "Funding Information: A.L.D. was supported by NSF Grant IIS-9820497. S.K. was supported by NSF Grant KDI-9980088. O.W. was supported by the Department of Energy Grant No. DE-FC02-95ER61962.A003. S.L.S. was supported by NSF Grant IIS-9902923 and NIH Grants R01 LM06845-01 and K01-HG00022-1. S.L.S. and A.L.D. were supported by NSF Grant IRI-9530462.",

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doi = "10.1093/nar/27.23.4636",

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T1 - Improved microbial gene identification with GLIMMER

AU - Delcher, Arthur L.

AU - Harmon, Douglas

AU - Kasif, Simon

AU - White, Owen

AU - Salzberg, Steven L.

N1 - Funding Information: A.L.D. was supported by NSF Grant IIS-9820497. S.K. was supported by NSF Grant KDI-9980088. O.W. was supported by the Department of Energy Grant No. DE-FC02-95ER61962.A003. S.L.S. was supported by NSF Grant IIS-9902923 and NIH Grants R01 LM06845-01 and K01-HG00022-1. S.L.S. and A.L.D. were supported by NSF Grant IRI-9530462.

PY - 1999/12/1

Y1 - 1999/12/1

N2 - The GLIMMER system for microbial gene identification finds ~ 97-98% of all genes in a genome when compared with published annotation. This paper reports on two new results: (i) significant technical improvements to GLIMMER that improve its accuracy still further, and (ii) a comprehensive evaluation that demonstrates that the accuracy of the system is likely to be higher than previously recognized. A significant proportion of the genes missed by the system appear to be hypothetical proteins whose existence is only supported by the predictions of other programs. When the analysis is restricted to genes that have significant homology to genes in other organisms, GLIMMER misses < 1% of known genes.

AB - The GLIMMER system for microbial gene identification finds ~ 97-98% of all genes in a genome when compared with published annotation. This paper reports on two new results: (i) significant technical improvements to GLIMMER that improve its accuracy still further, and (ii) a comprehensive evaluation that demonstrates that the accuracy of the system is likely to be higher than previously recognized. A significant proportion of the genes missed by the system appear to be hypothetical proteins whose existence is only supported by the predictions of other programs. When the analysis is restricted to genes that have significant homology to genes in other organisms, GLIMMER misses < 1% of known genes.

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Improved microbial gene identification with GLIMMER

Abstract

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