*biointelligence 16th feb2010*
*COBALT: A new tool for Multiple Sequence Alignment*
The simultaneous alignment of multiple sequences (*multiple alignment*)
serves as a building block in several fields of computational biology, such
as phylogenetic studies, detection of conserved motifs, prediction of
functional residues and secondary structure, prediction of correlations and
even quality assessment of protein sequences. For this an accurate multiple
sequence alignment tool was one of the biggest requirement from a long time.
* COBALT (Constraint based Multiple Alignment Tool)* is a
multiple sequence alignment tool that finds a collection of pairwise
constraints derived from conserved domain database, protein motif database,
and sequence similarity, using RPS-BLAST, BLASTP, and PHI-BLAST. Pairwise
constraints are then incorporated into a progressive multiple alignment.
COBALT has a general framework that uses progressive
multiple alignment to combine pairwise constraints from different sources
into a multiple alignment. COBALT does not attempt to use all available
constraints but uses only a high-scoring consistent subset that can change
as the alignment progresses, where a set of constraints is called consistent
if all of the constraints in the set can be simultaneously satisfied by a
multiple alignment. Using the RPS-BLAST tool, we can quickly search for
domains in CDD that match to regions of input sequences. When the same
domain matches to multiple sequences, we can infer several potential
pairwise constraints based on these domain matches. Furthermore, CDD also
contains auxiliary information that allows COBALT to create partial profiles
for input sequences before progressive alignment begins, and this avoids
computationally expensive procedures for building profiles.
COBALT has a general framework that uses progressive
multiple alignment to combine pairwise constraints from different sources
into a multiple alignment. COBALT does not attempt to use all available
constraints but uses only a high-scoring consistent subset that can change
as the alignment progresses, where a set of constraints is called consistent
if all of the constraints in the set can be simultaneously satisfied by a
multiple alignment. Using the RPS-BLAST tool, we can quickly search for
domains in CDD that match to regions of input sequences. When the same
domain matches to multiple sequences, we can infer several potential
pairwise constraints based on these domain matches. Furthermore, CDD also
contains auxiliary information that allows COBALT to create partial profiles
for input sequences before progressive alignment begins, and this avoids
computationally expensive procedures for building profiles.
COBALT is implemented in NCBI C++ Toolkit. More information on COBALT can be
found at:http://bioinformatics.oxfordjournals.org/cgi/content/full/23/9/1073
To access COBALT use this link:
http://www.ncbi.nlm.nih.gov/tools/cobalt/cobalt.cgi?link_loc=BlastHomeAd
*Regards,
Team Biointelligence
*
*Biointelligence*
*Getting started with biosciences*
*Website: www.biointelligence.in*
*Email: [email protected]
Tel: +91-731-425-7930*
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