Biology Reference
In-Depth Information
$ kalign-2.04 -i globin.fa -o globin-0.out -q -f
fasta
$ clustalo -i globin-0.out -o globin-1.out
This uses kalign to create a rough but high-speed initial
alignment, which is then refined using Clustal Omega.
It is always advisable to ensure whether input sequences are
actually aligned or not. In certain pipelines, unaligned sequences
are arranged in such a way that sequences are padded at the
end with gaps, such that all sequences have the same length.
This is interpreted by Clustal Omega as a valid alignment, while
in fact it is not. While the guide-tree that is derived from such
an input is useless at best, the HMM information that is derived
from this arrangement establishes the present, nonsensical,
alignment. In this case one could either remove all gaps from
the input by hand or specify the --dealign flag.
8. To align a single sequence to an existing profile use the
profile-profile syntax:
¼
¼
$ clustalo --profile1
globin1.aln --profile2
singleSequence.fa
When adding multiple sequences to a profile Clustal Omega
first aligns all the unaligned sequences, taking regard of the
HMM information derived from the profile, and then aligns
the newly formed profile to the already existing profile. If the
profile/sequences mode were to be used for adding a single
sequence, then Clustal Omega would complain because there is
only one sequence during the first round of alignments, which
cannot be aligned against any other sequence.
Conversely, to add unaligned sequences one-by-one to an
existing profile (rather than first aligning all the unaligned
sequences and then aligning the new and the old profiles) one
will have to distribute the unaligned sequences amongst multi-
ple files and align the single sequences to the profile, over-
writing the existing profile with the newly formed profile.
One possible (bash) implementation to do this might be:
while read label; do
read seq;
echo -e $label"\n"$seq
>
in.vie;
¼
¼
clustalo--p1
globin-0.aln--p2
in.vie-o globin-
0.aln--force;
done
<
unaligned.vie
where unaligned.vie is the file that contains the unaligned
sequence in Vienna format. Vienna format is the same as
Fasta format but where all the residue information is in one
(long) line. globin-0.aln is the file that originally contains the
existing profile. At every stage it is overwritten with the align-
ment comprising of the previous profile and one extra added
