TransAlign
Version 1.0 (1999)
A Java program package
for aligning coding nucleotide sequences according to the amino
acid sequence encoded. The package contains the two java commands
TranslateFastA and AddGapsFastA that can be invoked from the command-line.
Procedure
Aligning nucleotide sequences according to the encoded amino acid
sequence requires the following steps:
- Combine all nucleotide sequences to be aligned in a multiple
sequence file (only Pearson/FastA format is currently supported).
Ensure that every 3rd position is the start of a new codon.
Pseudogenes, i.e sequences with stop-codons or codons containing
gaps or ambiguous nucleotides are handled correctly, however
you must ensure that every third position denotes the start
of a codon.
- Use the TranslateFastA command to translate the nucleotide
sequences and create a multiple amino acid sequence file. This
ensures that both files are compatible. Codons containing stops,
gaps, or ambiguous characters are translated into gap characters
in the amino acid sequence.
- Use your preferred multiple sequence alignment method to align
the protein sequences. However, you must end up with a new Pearson/FastA
file containing the aligned sequences in the original order.
- Use the AddGapsFastA command provided in the package together
with the original nucleotide file and the aligned protein file
to create a new file with the nucleotide sequences aligned.
Stop codons and otherwise incomplete codons will remain and
reflect the original sequences.
Installing and
running the programs
In order to run the java programs TranslateFastA and AddGapsFastA
a Java Runtime Environment, (JRE) consisting of a Java Virtual
machine and supplementary files, must be installed on the system.
- Download a JRE and follow the instructions provided to install
it. You can freely optain a JRE for Windows 95/NT and Solaris
at http://java.sun.com/products/jdk/1.2/jre/
- Download the TransAlign package (file transalign.zip) here
. You do not need to unzip the file!
- You can now use the commands java -classpath transalign.zip
TranslateFastA and java -classpath transalign.zip AddGapsFastA
. Please note that java is case sensitive.
To simplify the syntax follow one of the two suggestions below:
- Create an environment classpath variable on your system and
set it to the path of transalign.zip.
- Unzip the file transalign.zip to a folder where the JRE expects
classfiles. This can either be the directory containing the
java.exe executable (example: c:\JavaSoft\Jre\1.2\bin) or any
other directory to which the classpath environment variable
points.
To set environment variables
in Windows 95 you can add the line classpath=c:\myjava_programs\transalign.zip
to your autoexecute.bat file. In Windows NT you can set environment
variables on the "Environment" tab of the "System" dialog box
in the "Control Panel".
You will now be able to
run the java programs using the commands java TranslateFastA and
java AddGapsFastA . This will result in a short help screen diplaying
other parameters required for program execution.
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