Introduction

GenomeComp is a tool for summarizing, parsing and visualizing the genome wide sequence comparison results derived from voluminous BLAST textual output, so as to locate the rearrangements, insertions or deletions of genome segments between species or strains.

It can be easily used to compare, parsing and visualize large genomic sequences, especially closely related genomes such as inter-species or inter-strains. In addition, it can also show other sequence features like repeat sequence distributions in one whole-genome DNA sequence by comparing the genome to itself.

It is a stand-alone graphical user interface (GUI) program which runs on Linux, Unix, Mac OS X (tested on version 10.2.4 only) and Microsoft Windows platforms and is written in Perl/Tk.

Releases (Last update: )

New: The second release of GenomeComp is available as following:

• Source code (0.13Mb) (build 041107) New
• Microsoft Windows (98/ME/NT/2000/XP) (1.27Mb)
• Linux 2 (1.43Mb)
• Solaris 2.6 (1.71Mb)
• IRIX 6.5 (1.95Mb)

The first release of GenomeComp is available in two distribution formats as following:

• Source code
  -- recommend for bioinformatists who are familiar with Perl

This is the original Perl code of this program, so the whole package is very portable (no more than 150Kb after compress). But you need Perl and Tk module installed on your system to run this program. (Click here to download)

• Executable binaries
  -- recommend for biologists and other general users

These are a set of compiled applications for some common operation systems separately. There are no any additional requirements for running the program, but the package size are more than 10 fold larger than the above.

• Microsoft Windows (98/ME/NT/2000/XP) (1.25Mb)
• Linux 2 (1.36Mb)
• Solaris 2.6 (1.66Mb)
• IRIX 6.5 (1.90Mb)

Documentation

The user manual explains how to install and run GenomeComp and the major parts of the program does. The HTML files for the manual are also available as a compressed UNIX tar file or a windows Zip file.

When you have comments about the manual please send them to the GenomeComp developers.

Reference

• Yang, J., Wang, J.H., Yao, Z.J., Jin, Q., Shen, Y., Chen, R.S., 2003. GenomeComp: a visualization tool for microbial genome comparison. J. Microbiol. Meth. 54, 423-426. <PDF (377 K)>

GenomeComp has been efficiently applied in comparison between different Shigella genomes (average genome size 4.6 Mbp) as well as against its close relatives, such as the non-pathogenic K-12 strain MG1655 (genome size 4.6 Mbp) and enterohemorrhagic O157:H7 strain EDL933 (genome size 5.5 Mbp) of Escherichia coli for the Shigella genome project in our center. See the following publications for more detail information about this.

• Yang, F., Yang, J., Zhang, X.B., Peng, J.P., Chen, L.H., Jiang, Y., Yan, Y.L., Tang, X.D., Wang, J., Xiong, Z.H., Dong, J., Xue, Y., Zhu, Y.F., Xu, X.Y., Sun, L.L., Chen, S.X., Nie, H., Xu, J.G., Wang, Y., Yuan, Z.H., Wen, Y.M., Yao, Z.J., Shen, Y., Qiang, B.Q., Hou, Y.D., Yu, J., Jin, Q., 2005. Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Nucleic Acids Res. 33, 6445-6458. <PDF (914 K)>
• Jin, Q., Yuan, Z., Xu, J., Wang, Y., Shen, Y., Lu, W., Wang, J., Liu, H., Yang, J., Yang, F., Zhang, X., Zhang, J., Yang, G., Wu, H., Qu, D., Dong, J., Sun, L., Xue, Y., Zhao, A., Gao, Y., Zhu, J., Kan, B., Ding, K., Chen, S., Cheng, H., Yao, Z., He, B., Chen, R., Ma, D., Qiang, B., Wen, Y., Hou, Y., Yu, J., 2002. Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res. 30, 4432-4441. <PDF (422 K)>

Acknowledgments

We thank Dr. Peter A. Noble and Mr. Erik Tribou (Department of Civil and Environmental Engineering, University of Washington) for help with testing the software on Mac OS X system.

The development of GenomeComp was funded by Chinese Academy of Sciences Grant No. KSCX2-2-07.

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