Detailed installation and Usage Instructions

Installation

The files that you download from the Download page are all gzipped (meaning compressed) except for the Windows binary which is just zipped.

For unix based platforms (Sun Solaris, SGI IRIX, Linux and Mac OSX), gunzip (meaning uncompress) the binary by issuing the following commands at the shell prompt:

prompt> gunzip mgalign-platform.gz

Replace the text "mgalign-platform.gz" with the filename of the binary that you download from the Download page. For example you should replace the text "mgalign-platform.gz" with "mgalign-linux.gz" if your platform is Linux. The effect of this process is that the filename has lost its ".gz" extension.

Then you have to give the binary execute permissions by issuing the following command, again at the shell prompt:

prompt> chmod 755 mgalign-platform

Again replace the text "mgalign-platform" with the filename of the binary (without the ".gz" extension, it has been removed in the decompression step). This results in a file that can be executed.

For the Window platform, make sure you have the program Winzip. If not get it from their main website at http://www.winzip.com. Then just extract the file to some folder on your computer.

Usage

MGAlign is usable only from the shell prompt (aka command prompt). You would first need to have two FASTA formatted files (example of a FASTA file). The issue the following command to perform the alignment:

prompt> ./mgalign-platform -g genomic.fasta -m mrna.fasta

Replace "mgalign-platform" with the filename of the binary (without the ".gz" extension). Replace "genomic.fasta" with a FASTA formatted file of your genomic sequence and "mrna.fasta" with a FASTA formatted file of your mRNA sequence.

The results of that alignment will appear in a while (or longer if the sequences are very long).

Output

MGAlign is able to produce two types of output as show below (click on image for a full sized version):

(A) Summary alignment output from MGAlign, giving details of the input sequences and the strand of the genomic sequence used in the alignment. The alignment number is also provided. In the event that there are several alignments generated by MGAlign (with the –allalign flag), all the alignments will be displayed, each having a different alignment number. A table lists the start and end of each aligned segment (exon) on the rRNA/EST and the genomic sequences together with the region flanking the slice junction (exonic regions in uppercase; introns in lowercase). The number of matches (mat), mismatches (mis) and gaps (gap) are also indicated for each exon. The lengths of mRNA/EST and genomic sequences are provided with the coverage of the alignment (%mRNA sequence that was successfully aligned). (B) Detailed MGAlign output format. Each line represents an exon in a comma-delimited format. The fields for each line consist of the alignment number, the mRNA/EST sequence filename, the genomic sequence filename, the start and end positions of the exon on the mRNA/EST sequence, the start and end positions of the exon on the genomic sequence, the number of basepair matches, the number of basepair mismatches, the number of gaps, the sequence of the exon on the mRNA/EST sequence and the sequence of the exon on the genomic sequence respectively. The sequence field shown above is truncated due to space constraints, so only part of the sequence of the exon on the mRNA/EST sequence is shown.

More Information

For more information, consult the README file