Readme file for MGAlign 26th Dec 2002

Usage

The usage of the program is pretty simple. You need to specify two FASTA formatted sequence files as options to the 
program as shown below:

mgalign -g genomic_sequence_file.fasta -m mRNA_sequence_file.fasta

The file after the switch "-g" is the genomic sequence file. This file contains the genomic sequence in FASTA format. The 
file after the switch "-m" is the mRNA sequence file. This file contains the mRNA/EST sequence in FASTA format. The 
genomic sequence should be longer than the mRNA sequence else the program will exit with an error.

There are two output formats specified using the switch "-o". A numeric one ("1") after this switch specifies a listing 
output, which is basically a listing of the start and end positions of the exon. A numeric two ("2") after the "-o" 
switch specific a comma delimiting format which is easily parsed by a computer program. Each line represents a single 
exon. The meaning of the various fields are as follows:

Field	Meaning
1	mRNA sequence file name
2	Genomic sequence file name
3	Orientation of aligned mRNA sequence. "0" for normal orientation and "1" for reversed complemented orientation
4	Starting position of exon based on mRNA sequence. Note that the positions start from 0.
5	Ending position of exon based on mRNA sequnece. Note that the positions start from 0.
6	Starting position of exon based on genomic sequence. Note that the positions start from 0.
7	Ending position of exon based on genomic sequence. Note that the positions start from 0.
8	Number of matches in the exon alignment.
9	Number of mismatch in the exon alignment.
10	Number of gaps in the exon alignment.
11	The aligned mRNA sequence.
12	The aligned genomise sequence.

Contact

Any comments or suggestions are greatly appreciated. You can forward them to Bernett Lee at bernett@bic.nus.edu.sg