Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2006 Dec 12;7 Suppl 4(Suppl 4):S18.
doi: 10.1186/1471-2105-7-S4-S18.

GenomeBlast: a web tool for small genome comparison

Guoqing Lu  1 , Liying Jiang, Resa M K Helikar, Thaine W Rowley, Luwen Zhang, Xianfeng Chen, Etsuko N Moriyama
Affiliations

GenomeBlast: a web tool for small genome comparison

Guoqing Lu et al. BMC Bioinformatics. .

Abstract

Background: Comparative genomics has become an essential approach for identifying homologous gene candidates and their functions, and for studying genome evolution. There are many tools available for genome comparisons. Unfortunately, most of them are not applicable for the identification of unique genes and the inference of phylogenetic relationships in a given set of genomes.

Results: GenomeBlast is a Web tool developed for comparative analysis of multiple small genomes. A new parameter called "coverage" was introduced and used along with sequence identity to evaluate global similarity between genes. With GenomeBlast, the following results can be obtained: (1) unique genes in each genome; (2) homologous gene candidates among compared genomes; (3) 2D plots of homologous gene candidates along the all pairwise genome comparisons; and (4) a table of gene presence/absence information and a genome phylogeny. We demonstrated the functions in GenomeBlast with an example of multiple herpesviral genome analysis and illustrated how GenomeBlast is useful for small genome comparison.

Conclusion: We developed a Web tool for comparative analysis of small genomes, which allows the user not only to identify unique genes and homologous gene candidates among multiple genomes, but also to view their graphical distributions on genomes, and to reconstruct genome phylogeny. GenomeBlast runs on a Linux server with 4 CPUs and 4 GB memory. The online version of GenomeBlast is available to public by using a Web browser with the URL http://bioinfo-srv1.awh.unomaha.edu/genomeblast/.

PubMed Disclaimer

Figures

Figure 1
Figure 1
The architecture of GenomeBlast. GenomeBlast consists of sequence extraction, database formatting, sequence comparison, output filtering, and visual presentation of results. The inputs to GenomeBlast are genome sequences in the GenBank format, each in a single file. The outputs include three-level results: 1) putative unique genes and homologous genes; 2) 2D plots of homologous gene candidates for pairwise genome comparisons; 3) a table of gene presence/absence information, genome phylogeny, and a summary table for multiple genome comparison.
Figure 2
Figure 2
A possible output generated by the blast program. The blast program may find two or more highly similar regions of the same subject sequence, which need to be combined before we can evaluate global sequence similarity between the query and the subject sequence.
Figure 3
Figure 3
Output window of putative unique genes. Two alpha herpesviruses, EBV and EHV2, were selected for comparison. A total of 45 and 38 unique CDS candidates were found in EBV and EHV2, respectively.
Figure 4
Figure 4
Output window of putative homologous genes. EBV and EHV2 were selected for comparison. 82 homologous CDS candidates were identified between them.
Figure 5
Figure 5
A 2D plot of homologous gene candidates in genomes. EBV and EHV2 were selected for comparison. The plot shows the distribution of homologous CDS on EBV and EHV2 genomes. The threshold values used for homologous CDS identification and the color scheme for identity representation are illustrated.
Figure 6
Figure 6
Genome phylogeny among the herpes viruses. The 13 herpesviral genomes described in [1, 4] were used for phylogeny inference. Panel A was generated from GenomeBlast, whereas Panel B was produced with the TreeView program using the same tree file from GenomeBlast.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Alba MM, Das R, Orengo CA, Kellam P. Genomewide function conservation and phylogeny in the Herpesviridae. Genome Res. 2001;11:43–54. doi: 10.1101/gr.149801. - DOI - PMC - PubMed
    1. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. Versatile and open software for comparing large genomes. Genome Biol. 2004;5:R12. doi: 10.1186/gb-2004-5-2-r12. - DOI - PMC - PubMed
    1. Florea L, Riemer C, Schwartz S, Zhang Z, Stojanovic N, Miller W, McClelland M. Web-based visualization tools for bacterial genome alignments. Nucleic Acids Res. 2000;28:3486–3496. doi: 10.1093/nar/28.18.3486. - DOI - PMC - PubMed
    1. Montague MG, Hutchison CA., 3rd Gene content phylogeny of herpesviruses. Proc Natl Acad Sci U S A. 2000;97:5334–5339. doi: 10.1073/pnas.97.10.5334. - DOI - PMC - PubMed
    1. Yang S, Doolittle RF, Bourne PE. Phylogeny determined by protein domain content. Proc Natl Acad Sci U S A. 2005;102:373–378. doi: 10.1073/pnas.0408810102. - DOI - PMC - PubMed

Publication types

LinkOut - more resources