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News

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!

Introduction

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 mechanism.

The program is faster than other heuristic based programs like Sim4 and Spidey (comparison results). 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 systems.

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 includes:

  • 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 bernett@bic.nus.edu.sg.

 

 National University of Singapore[Python Powered]
 Department of Biochemistry