17 February 2004 - The server is up online. Thanks for your patience!
15 January 2004 - The server has crashed. We are recovering right now,
but it could take a while. Sorry for the inconvenience.
22 December 2003 - A page on the methodology is available.
19 November 2003 - Pseudocodes for MGAlign available as Pseudocodes.pdf. Flowchart also available as Flowchart.gif.
17 November 2003 - Detailed methodology of MGAlign available as Methodology.pdf.
2nd October 2003 - New binaries (version 1.3.7) are available for download and copies of the datasets are available on the comparison page!
MGAlign (short for mRNA to Genome Alignments)
is a program written to quickly and accurately align mRNA
sequences to genomic sequences on a personal computer.
This program is useful for the determination of exon arrangements
of genes. The arrangement of exons for genes is important
as we know that in eukaryotes, one gene can have many
products due to mRNA splicing. Thus the knowledge of the
exon arrangement is vital for understanding of the splicing
The program is faster than other
heuristic based programs like Sim4
MGAlign achieves this speed by doing an initial search
that reduces the search space for subsequent searches.
The program also outputs a format which is easily parsed
by computer programs allowing for easy creation of a new
output format as well as ease of integration into larger
The program is available as binaries
for a number of platforms. There is also a web
service at this website. The web service allows for
simple analysis such as 6 frame translation, pattern searching
and links to BLAST service. The web service also provides
results in the form of FASTA files and GenBank files for
further analysis using other programs.
Future improvements to the web service
- Ability to use GI Accession
numbers instead of FASTA sequences.
- Alignment and visualization
of multiple mRNA/EST sequences.
- Ability to perform pattern search
over multiple exons and introns.
For more information, contact firstname.lastname@example.org.