Biology Reference
In-Depth Information
Fig. 3 Example MSA produced by MSAProbs in multi-FASTA format
Fig. 4 Example MSA produced by MSAProbs in CLUSTAL format
MSAProbs takes as input protein sequences in multi-FASTA
format. The resulting alignments can be displayed in either multi-
FASTA format or CLUSTAL format. Typical usages of the program
(on Linux) can be as follows:
l
msaprobs infile >outfile
l
msaprobs infile -o outfile
l
msaprobs -num_threads 4 infile1 infile2
In the following, we show how to use MSAProbs to construct
MSA by taking the alignment of four sequences from BAliBASE
3.0 [
5
] as an example. The default settings are used to produce the
multiple alignments. Figures
3
and
4
illustrate the resulting align-
ments in multi-FASTA format and CLUSTAL format, respectively,
where the used command lines are “
msaprobs infile
” and “
msaprobs
infile -clustalw
,” respectively.
As mentioned above, we have parallelized MSAProbs using multi-
threading to accelerate the construction of MSA on multi-core
CPUs. In the following, we have used a protein sequence dataset,
3.6 Parallel
Scalability
