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GeneOrder3.0: software for comparing the order of genes in pairs of small bacterial genomes.

Celamkoti S, Kundeti S, Purkayastha A, Mazumder R, Buck C, Seto D - BMC Bioinformatics (2004)

Bottom Line: GeneOrder3.0 has been developed and validated successfully on several small bacterial genomes (ca. 580 kb to 1.83 Mb) archived in the NCBI GenBank database.Whole genome alignments of genes are presented in both a table and a dot plot.This allows the detection of evolutionary more distant relationships since protein sequences are more conserved than DNA sequences.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics and Computational Biology, School of Computational Sciences, George Mason University, 10900 University Boulevard, MSN 5B3, Manassas, VA 20110, USA. scelamko@gmu.edu

ABSTRACT

Background: An increasing number of whole viral and bacterial genomes are being sequenced and deposited in public databases. In parallel to the mounting interest in whole genomes, the number of whole genome analyses software tools is also increasing. GeneOrder was originally developed to provide an analysis of genes between two genomes, allowing visualization of gene order and synteny comparisons of any small genomes. It was originally developed for comparing virus, mitochondrion and chloroplast genomes. This is now extended to small bacterial genomes of sizes less than 2 Mb.

Results: GeneOrder3.0 has been developed and validated successfully on several small bacterial genomes (ca. 580 kb to 1.83 Mb) archived in the NCBI GenBank database. It is an updated web-based "on-the-fly" computational tool allowing gene order and synteny comparisons of any two small bacterial genomes. Analyses of several bacterial genomes show that a large amount of gene and genome re-arrangement occurs, as seen with earlier DNA software tools. This can be displayed at the protein level using GeneOrder3.0. Whole genome alignments of genes are presented in both a table and a dot plot. This allows the detection of evolutionary more distant relationships since protein sequences are more conserved than DNA sequences.

Conclusions: GeneOrder3.0 allows researchers to perform comparative analysis of gene order and synteny in genomes of sizes up to 2 Mb "on-the-fly."

Availability: http://binf.gmu.edu/genometools.html and http://pasteur.atcc.org:8050/GeneOrder3.0.

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Related in: MedlinePlus

GeneOrder3.0 analysis of Mycoplasma genitalium (NC_000908) versus Mycoplasma pneumoniae (NC_000912). BLAST scores are set at the defaults of 200, 100 and 75 as represented by the dots, crosses and open squares, respectively.
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Figure 1: GeneOrder3.0 analysis of Mycoplasma genitalium (NC_000908) versus Mycoplasma pneumoniae (NC_000912). BLAST scores are set at the defaults of 200, 100 and 75 as represented by the dots, crosses and open squares, respectively.

Mentions: Figure 1 shows an analysis of M. genitalium with M. pneumoniae. From this display of the relative arrangements of coding sequences we can easily see that gene order and synteny have been largely maintained between the two organisms. Portions of the genomes (specifically genes from '100–300' region of the organisms) have been translocated. There are two large gaps in the diagonal at this region; a perfect diagonal represents perfect synteny. These gaps appear to be a result of translocations of segments of the chromosome. Individual genes that are highly conserved but nevertheless have moved are also seen as red dots (BLAST score 200+) away from the diagonal. In addition, there are several crosses and squares (representing BLAST score ranges of '100–200' and '75–100,' respectively) that putatively represent fast evolving genes, and therefore may be involved in specialized or adaptive functions such as pathogenesis. In addition, genes aligned horizontally or perpendicularly may represent potentially, but not necessarily, related genes. A careful and detailed analysis of the graph generated by GeneOrder3.0 reveals several genes that can be investigated further to understand better the species-specific differences of the two organisms. This allows the researcher to home in on potential reasons of specialization and adaptations.


GeneOrder3.0: software for comparing the order of genes in pairs of small bacterial genomes.

Celamkoti S, Kundeti S, Purkayastha A, Mazumder R, Buck C, Seto D - BMC Bioinformatics (2004)

GeneOrder3.0 analysis of Mycoplasma genitalium (NC_000908) versus Mycoplasma pneumoniae (NC_000912). BLAST scores are set at the defaults of 200, 100 and 75 as represented by the dots, crosses and open squares, respectively.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC419981&req=5

Figure 1: GeneOrder3.0 analysis of Mycoplasma genitalium (NC_000908) versus Mycoplasma pneumoniae (NC_000912). BLAST scores are set at the defaults of 200, 100 and 75 as represented by the dots, crosses and open squares, respectively.
Mentions: Figure 1 shows an analysis of M. genitalium with M. pneumoniae. From this display of the relative arrangements of coding sequences we can easily see that gene order and synteny have been largely maintained between the two organisms. Portions of the genomes (specifically genes from '100–300' region of the organisms) have been translocated. There are two large gaps in the diagonal at this region; a perfect diagonal represents perfect synteny. These gaps appear to be a result of translocations of segments of the chromosome. Individual genes that are highly conserved but nevertheless have moved are also seen as red dots (BLAST score 200+) away from the diagonal. In addition, there are several crosses and squares (representing BLAST score ranges of '100–200' and '75–100,' respectively) that putatively represent fast evolving genes, and therefore may be involved in specialized or adaptive functions such as pathogenesis. In addition, genes aligned horizontally or perpendicularly may represent potentially, but not necessarily, related genes. A careful and detailed analysis of the graph generated by GeneOrder3.0 reveals several genes that can be investigated further to understand better the species-specific differences of the two organisms. This allows the researcher to home in on potential reasons of specialization and adaptations.

Bottom Line: GeneOrder3.0 has been developed and validated successfully on several small bacterial genomes (ca. 580 kb to 1.83 Mb) archived in the NCBI GenBank database.Whole genome alignments of genes are presented in both a table and a dot plot.This allows the detection of evolutionary more distant relationships since protein sequences are more conserved than DNA sequences.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics and Computational Biology, School of Computational Sciences, George Mason University, 10900 University Boulevard, MSN 5B3, Manassas, VA 20110, USA. scelamko@gmu.edu

ABSTRACT

Background: An increasing number of whole viral and bacterial genomes are being sequenced and deposited in public databases. In parallel to the mounting interest in whole genomes, the number of whole genome analyses software tools is also increasing. GeneOrder was originally developed to provide an analysis of genes between two genomes, allowing visualization of gene order and synteny comparisons of any small genomes. It was originally developed for comparing virus, mitochondrion and chloroplast genomes. This is now extended to small bacterial genomes of sizes less than 2 Mb.

Results: GeneOrder3.0 has been developed and validated successfully on several small bacterial genomes (ca. 580 kb to 1.83 Mb) archived in the NCBI GenBank database. It is an updated web-based "on-the-fly" computational tool allowing gene order and synteny comparisons of any two small bacterial genomes. Analyses of several bacterial genomes show that a large amount of gene and genome re-arrangement occurs, as seen with earlier DNA software tools. This can be displayed at the protein level using GeneOrder3.0. Whole genome alignments of genes are presented in both a table and a dot plot. This allows the detection of evolutionary more distant relationships since protein sequences are more conserved than DNA sequences.

Conclusions: GeneOrder3.0 allows researchers to perform comparative analysis of gene order and synteny in genomes of sizes up to 2 Mb "on-the-fly."

Availability: http://binf.gmu.edu/genometools.html and http://pasteur.atcc.org:8050/GeneOrder3.0.

Show MeSH
Related in: MedlinePlus