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1. Introduction to GenomeComp
What is GenomeComp?GenomeComp is a DNA sequence comparison tool and graphical user interface (GUI) viewer implemented in Perl/Tk. It can read one, two or three input sequences in either of FASTA, GENBANK or EMBL format, then it runs the external program BLASTN or MegaBlast to do the comparison between paired sequences in background. If the results already exist, it can skip that step and read the output file directly. Then the dynamic display of the results will show in the canvas of the main window. GenomeComp can easily manage genome wide sequences (about several mega base pairs), so as to locate the rearrangements, insertions or deletions of genome segments between species or strains. In addition, it can show other features like repeat sequence distribution in one whole-genome sequence by self-comprison. System RequirementsGenomeComp will run on any Unix/Linux, Mac OS X (tested on version 10.2.4 only) or Windows system ) that has a recent version of Perl with Tk module installed. For Unix/Linux systems Perl version 5.6 (or higher) and Tk version 800.022 (or higher) is recommend. While for MicroSoft Windows systems ActivePerl 521 (or higher) and Tk800.022 (or higher) is recommend. Most of the orginal development has been done using Perl 5.004 with Tk 800.022 on an IRIX 6.5 system. The second release was developped mainly on a RedHat Linux 8.0 system with Perl 5.8 and Tk 804.024. Also RedHat Linux 7.0 system with Perl 5.6.0 and Tk 800.015, and Windows 98 and 2000 professional system with ActivePerl 521 and Tk 800.022 have been tested successful with the first release. However, the second release require at lease Tk800.022 to run! New: The binary distributions of this program, which have no any system requirements, are available now! (Please visit GenomeComp home page for details.) In comparison of microbial genomes (several million base pairs in length), we have not found technical difficulty as long as sufficient system memory is available. To the current release, the average memory cost for comparing general annotated genome sequences (i.e. GenBank or EMBL format) is about 5Mb/Mbp/sequence. For example, the whole genome comparison between E. coli K12 and S. flexneri 2a 301 (both are about 4.7Mbp) used nearly 50Mb memories in my Linux when testing. The comparison speed should mainly determined by the CPU speed of running system besides the size of the input sequences. On my Linux (Intel P4 1.5G), the above mentioned comparison needed only about half minute with an existing BLAST output file. Getting and Installing GenomeComp The most up to date version of GenomeComp is always available from the GenomeComp home page. Please skip the following contents of this part if you are using the binary distribution of this program. For source code distribution users, before installing GenomeComp you should make sure that your system have Perl and Tk module installed. Unix/Linux systems usually have Perl installed when the systems were setup. If that, users can easily get it's version information by typing "perl -v" on command line (Of course Windows users also can use this method to test if Perl has been installed). Otherwise, go to the web page of Perl Ports (Binary Distributions) from CPAN, download and install the suitable binary version of Perl according to your system type. And the Tk module is available also on the CPAN site by searching the distribution called Tk or from the author's home page. Windows users also can get the suitable distributions of Perl and Tk from CPAN's web site just like the above. But the more convenient and recommended way is to go directly to the ActiveState web site to get the recent version of ActivePerl for MSWin32 from the ActivePerl download page and the corresponding Tk module from the PPM Zip Archieves download page. Installation Instructions for Unix/Linux
Installation Instructions for Mac OS X
Installation Instructions for Windows
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Copyright
@2002 Chinese National Human Genome Center,Beijing
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