Phylogenomics -
a "how to" overview
A
phylogenetic tree is constructed in the following basic steps:
-
Selection of a DNA or protein sequence of
interest
-
Identification of related sequences by database
searches
-
Alignment of the sequence
-
Construction of a tree by the use of the
resulting alignment
Several
computer programs are available for database searches. Multiple searches
using different programs should be performed, since the programs differ
in their sensitivity (1). A good alignment is a prerequisite for a meaningful
phylogenetic tree. At this step it is also important, to use more than
one program to obtain an optimal alignment (2). There are also different
methods and programs for construction of phylogenetic trees, which can
vary significantly in computational speed. The phylogenetic trees obtained
by the different combinations of methods are usually stored in database
in different formats (machine readable, image).
However,
the interplay between the different applications is automated only in special
instances (3, 4). For large scale phylogenomic studies, it will be absolutely
necessary to streamline the whole process. Furthermore, due to the rapid
increase of available genome sequences, the generation of phylogenetic
trees should be repeated in appropriate time intervals in order to update
the tree databases.
It
should be also noted that the currently available tree building algorithms
are not optimized for inferring phylogenetic relationships. However, reasonably
good results are obtained using the currently available programs. Nevertheless,
development of novel algorithms, optimized for the phylogenomics approach,
is highly desirable.
(1)
Brenner, S.E., Chotia, C., and Hubbard, T.J.P. 1998. Proc. Natl. Acad.
Sci. 95: 6073-6078.
(2)Thompson,
J.D., Plewniak, F., and Poch, O. 1999. Nucleic Acids Res. 27: 2682-2690.
(3)
Sicheritz-Pontén, T., and Andersson, S.G.E. 2001. Nucleic Acids
Res. 29: 545-552.
(4) Zmasek, C.M., and Eddy, S.R. 2001.
Bioinformatics 17: 821-828.
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