Import Window : Algorithms Commands
Block align single
The block alignment algorithm is a new alignment method being developed at NCBI.
Briefly, it uses a dynamic programming algorithm, except the alignment is created
by searching with whole (gapless) blocks - corresponding to the blocks of the alignment in Cn3D -
rather than one residue at a time as in traditional sequence alignments. See Kann M.G. et. al., Bioinformatics, 2005 Apr 15, 21(8):1451-6
(PMID 15613392).
The block alignment options panel contains numeric fields that correspond
to the parameters of the block alignment algorithm.
The options at the bottom are: Global alignment to switch between
global and local alignment modes, Merge to either never merge, merge in each
succesfully aligned row into the multiple alignment and recalculate the PSSM
before proceeding with the next alignment, or merge after all alignments are completed,
and Keep existing blocks to control
whether to freeze the alignment of existing blocks (as opposed to always
realigning all blocks).
Block align N
Like Block align single, except it attempts to run
the block alignment algorithm on the first N import alignments; you will be prompted for how many (N)
sequences to realign.
BLAST single
Uses NCBI's BLAST-two-sequences algorithm with default parameters to align an import sequence
to the current first sequence of the multiple alignment, discarding any existing alignment. This is not
intended as a complete interface to the BLAST algorithm, but only to provide a
starting point for aligning a new sequence. See NCBI's BLAST web pages for more
complete BLAST functionality. The aligned region on the principal sequence will be
limited to the aligned region in the multiple alignment window, if there is a
multiple alignment present. The aligned region on the imported sequence will be
unlimited, unless this sequence has been demoted from the multiple alignment, in
which case the original aligned region is used as a guide. The sequence's aligned
region can also be set manually using the Set region
command.
BLAST/PSSM single
Similar to BLAST single, except that a sequence
to profile BLAST alignment is performed, using a profile constructed from the
current multiple alignment. Aligned region restrictions are the same as
described above.
BLAST neighbor
Computes BLAST-two-sequences for the import and all rows of the multiple alignment. The highest scoring such pairwise alignment
is then used to infer an alignment of the import with the principal sequence of the multiple alignment, and the import is merged
accordingly.
Thread single
This command is used to align a single sequence to the first structure of the multiple alignment,
using NCBI's threading algorithm. When you select this item and then click on
a sequence pair, a threading options panel comes up. A complete discussion of
this algorithm and the details of these settings is beyond the scope of this document,
and in many cases the default numerical values will be adequate. If Merge results
is checked, then if the results of threading yield an alignment compatible with
the current multiple alignment, then the new alignment will be merged in. If Freeze
blocks is checked, then block boundaries that are not adjacent to realigned
blocks are not allowed to move, which saves time in the threader.
Thread all
This has the same effect as thread single, except
it will run the threader on all sequences in the import window, merging each one
after it is threaded if Merge results is on.
Extend single
This algorithm simply grows blocks of the selected sequence
to either side, regardless of residue identity or any scoring, attempting only to make
blocks (just) large enough so that the import alignment can be merged into the multiple alignment. It will stop if there is
any ambiguity - for example where blocks on either side of a short insert would "compete" for residues.
Extend all
Same as extend single, except extension is performed on all import sequences.
Set region
Used to set the region of an imported sequence that is allowed to be aligned. This is useful, for example, if the imported sequence contains repeated regions
and you'd like to construct an alignment across a specific repeat.
Reset all regions
Reset all regions on all sequences, so that alignments are unrestricted.