Biology Reference
In-Depth Information
¼
$ clustalo -i globin.fa -o globin.sto --outfmt
st
If the file globin.sto does not exist, then Clustal Omega reads
the sequence file globin.fa, aligns the sequences and prints the
result to globin.sto in Stockholm format. If the file globin.sto
does exist already, then Clustal Omega terminates the alignment
process before reading globin.fa.
$ clustalo -i globin.fa -o globin.aln --outfmt
¼
clu
--force
Clustal Omega reads the sequence file globin.fa, aligns the
sequences and prints the result to globin.aln in Clustal format,
overwriting the file globin.aln, if it already exists.
¼
$ clustalo -i globin.fa --guidetree-out
globin.dnd
--force
Clustal Omega reads the sequence file globin.fa, aligns the
sequences, prints the result to screen in fasta/a2m format (default)
and the guide-tree to globin.dnd, overwriting this file if it already
exists ( see Notes 5 and 6 ).
$ clustalo -i globin.fa --guidetree-in
globin.dnd
Clustal Omega reads the files globin.fa and globin.dnd, skip-
ping distance calculation and guide-tree creation, using instead the
guide-tree specified in globin.dnd. The alignment is outputted to
screen in fasta format.
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As mentioned in Subheading 1 Clustal Omega is a progressive
aligner. This means that residues that are aligned and gaps that
are positioned during an early stage of the alignment process
remain fixed throughout the rest of the process and cannot be
changed. An alignment of two residues that appears to be advanta-
geous at an early stage may indeed turn out to be suboptimal in the
later alignments. External Profile Alignment (EPA) is a way to
provide the alignment process with a certain degree of “foresight.”
If the final alignment can be anticipated, then this prior knowledge
can be encoded as a HMM. This may be, because the user knows
they are aligning, for example, globins. Precomputed HMMs for
globins are available from repositories such as Pfam ( http://pfam.
sanger.ac.uk/ ) . Alternatively, the user could have produced a man-
ually curated high-quality alignment of sequences that are homol-
ogous to the input set. This alignment can then be converted into a
HMM using, for example, HMMER [ 8 ].
Clustal Omega accepts these external profiles-HMMs as input,
accompanying the unaligned sequences. During the alignment
stage sequences and profiles are first aligned to the external profile,
and pseudo-counts from the HMM are transferred to the internal
HMM used to align the sequences progressively. The desired effect
of this is to “nudge” particular residues and gaps towards the
position where they are expected to end up in the final alignment.
3.2 External Profile
Alignment (EPA)
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