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A tool for repetitive
sequencing projects |
Many DNA sequencing
projects involve obtaining the sequence of
the same gene fragment, or multiple gene fragments,
from large numbers of strains of a species
or from a number of different species.
These include
multilocus sequence typing (MLST) for the unambiguous
characterisation of strains of bacterial species
(Maiden et al., 1998), multilocus sequence
analysis (MLSA) for defining and circumscribing
closely-related species (Gevers et al., 2005;
Hanage, Fraser and Spratt, 2006), and many phylogenetic
studies. In
these approaches sequences are often obtained
for the forward and reverse strand of a gene
fragment for sets of 96 (or more) strains at
a time using a microtitre dish format. The
sequences of both strands from the set of strains
then need to be aligned, trimmed to defined
start and end points, and any ambiguities resolved. In
addition, the trace files, the corresponding
strain name and its associated edited sequences,
need to be stored within a database, and the
data need to be exported to other programs
or used to interrogate other databases.
We
have developed a free software package, Phineus,
to provide a user-friendly pipeline which is
designed to rapidly perform these steps for
sets of 96 sequences. The program also links
to MLST databases allowing automation of the
steps from trace file to allele assignment.
References
Maiden, M.C.J.,
Bygraves, J.A., Feil, E., Morelli, G., Russell,
J.E., Urwin, R., Zhang, Q., Zhou, J., Zurth,
K., Caugant, D.A., Feavers, I.M., Achtman,
M., and Spratt, B.G. 1998.
Multilocus sequence typing: a portable approach
to the identification of clones within populations
of pathogenic microorganisms. Proc.
Natl. Acad. Sci. USA, 95:
3140-3145.PMID:9501229
Gevers, D, Cohan, F, Lawrence, J., Spratt,
B.G., Coenye, T., Feil, E.J, Stackebrandt,
E., Manfio, G., Van de Peer, Y., Nesme, X.,
Thompson, F. and Swings, J. 2005.
Re-evaluating bacterial species. Nature
Microbiol. Rev. 3: 733-739.PMID:16138101 Hanage, W.P., Fraser, C. and
Spratt, B.G. Sequences,
sequence clusters and bacterial species. 2006. Phil.
Trans. Roy. Soc. Ser. B., 361:1917-27.PMID:17062411 |
