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galaxieEST: addressing EST identity through automated phylogenetic analysis

Nilsson, R H; Rajashekar, Balaji LU ; Larsson, K H and Ursing, B M (2004) In BMC Bioinformatics 5.
Abstract
Background: Research involving expressed sequence tags ( ESTs) is intricately coupled to the existence of large, well-annotated sequence repositories. Comparatively complete and satisfactory annotated public sequence libraries are, however, available only for a limited range of organisms, rendering the absence of sequences and gene structure information a tangible problem for those working with taxa lacking an EST or genome sequencing project. Paralogous genes belonging to the same gene family but distinguished by derived characteristics are particularly prone to misidentification and erroneous annotation; high but incomplete levels of sequence similarity are typically difficult to interpret and have formed the basis of many... (More)
Background: Research involving expressed sequence tags ( ESTs) is intricately coupled to the existence of large, well-annotated sequence repositories. Comparatively complete and satisfactory annotated public sequence libraries are, however, available only for a limited range of organisms, rendering the absence of sequences and gene structure information a tangible problem for those working with taxa lacking an EST or genome sequencing project. Paralogous genes belonging to the same gene family but distinguished by derived characteristics are particularly prone to misidentification and erroneous annotation; high but incomplete levels of sequence similarity are typically difficult to interpret and have formed the basis of many unsubstantiated assumptions of orthology. In these cases, a phylogenetic study of the query sequence together with the most similar sequences in the database may be of great value to the identification process. In order to facilitate this laborious procedure, a project to employ automated phylogenetic analysis in the identification of ESTs was initiated. Results: galaxieEST is an open source Perl-CGI script package designed to complement traditional similarity-based identification of EST sequences through employment of automated phylogenetic analysis. It uses a series of BLAST runs as a sieve to retrieve nucleotide and protein sequences for inclusion in neighbour joining and parsimony analyses; the output includes the BLAST output, the results of the phylogenetic analyses, and the corresponding multiple alignments. galaxieEST is available as an on-line web service for identification of fungal ESTs and for download/local installation for use with any organism group at http://galaxie.cgb.ki.se/galaxieEST.html. Conclusions: By addressing sequence relatedness in addition to similarity, galaxieEST provides an integrative view on EST origin and identity, which may prove particularly useful in cases where similarity searches return one or more pertinent, but not full, matches and additional information on the query EST is needed. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
BMC Bioinformatics
volume
5
publisher
BioMed Central
external identifiers
  • pmid:15236648
  • wos:000222827200001
  • scopus:13244279477
ISSN
1471-2105
DOI
10.1186/1471-2105-5-87
language
English
LU publication?
yes
id
ffc1ec61-5acc-4371-9295-60b0fffd8e1c (old id 135640)
date added to LUP
2007-06-29 13:46:56
date last changed
2017-01-01 06:37:41
@article{ffc1ec61-5acc-4371-9295-60b0fffd8e1c,
  abstract     = {Background: Research involving expressed sequence tags ( ESTs) is intricately coupled to the existence of large, well-annotated sequence repositories. Comparatively complete and satisfactory annotated public sequence libraries are, however, available only for a limited range of organisms, rendering the absence of sequences and gene structure information a tangible problem for those working with taxa lacking an EST or genome sequencing project. Paralogous genes belonging to the same gene family but distinguished by derived characteristics are particularly prone to misidentification and erroneous annotation; high but incomplete levels of sequence similarity are typically difficult to interpret and have formed the basis of many unsubstantiated assumptions of orthology. In these cases, a phylogenetic study of the query sequence together with the most similar sequences in the database may be of great value to the identification process. In order to facilitate this laborious procedure, a project to employ automated phylogenetic analysis in the identification of ESTs was initiated. Results: galaxieEST is an open source Perl-CGI script package designed to complement traditional similarity-based identification of EST sequences through employment of automated phylogenetic analysis. It uses a series of BLAST runs as a sieve to retrieve nucleotide and protein sequences for inclusion in neighbour joining and parsimony analyses; the output includes the BLAST output, the results of the phylogenetic analyses, and the corresponding multiple alignments. galaxieEST is available as an on-line web service for identification of fungal ESTs and for download/local installation for use with any organism group at http://galaxie.cgb.ki.se/galaxieEST.html. Conclusions: By addressing sequence relatedness in addition to similarity, galaxieEST provides an integrative view on EST origin and identity, which may prove particularly useful in cases where similarity searches return one or more pertinent, but not full, matches and additional information on the query EST is needed.},
  author       = {Nilsson, R H and Rajashekar, Balaji and Larsson, K H and Ursing, B M},
  issn         = {1471-2105},
  language     = {eng},
  publisher    = {BioMed Central},
  series       = {BMC Bioinformatics},
  title        = {galaxieEST: addressing EST identity through automated phylogenetic analysis},
  url          = {http://dx.doi.org/10.1186/1471-2105-5-87},
  volume       = {5},
  year         = {2004},
}