PubDNA Finder: a web database linking full-text articles to sequences of nucleic acids.
CONCLUSIONS
PubDNA Finder is an online repository that we have created to link PubMed Central manuscripts to the sequences of nucleic acids appearing in them. It extends the search capabilities provided by PubMed Central by enabling researchers to perform advanced searches involving sequences of nucleic acids. This includes, among other features (i) searching for papers mentioning one or more specific sequences of nucleic acids and (ii) retrieving the genetic sequences appearing in different articles. These additional query capabilities are provided by a searchable index that we created by using the full text of the 176 672 papers available at PubMed Central at the time of writing and the sequences of nucleic acids appearing in them. To automatically extract the genetic sequences occurring in each paper, we used an original method we have developed. The database is updated monthly by automatically connecting to the PubMed Central FTP site to retrieve and index new manuscripts. Users can query the database via the web interface provided.


BACKGROUND
PubDNA Finder can be freely accessed at http://servet.dia.fi.upm.es:8080/pubdnafinder
García-Remesal
Miguel
M
Departamento de Inteligencia Artificial, Facultad de Informática, Universidad Politécnica de Madrid, Campus de Montegacedo S/N, Boadilla del Monte, Madrid, Spain. mgarcia@infomed.dia.fi.upm.es
Cuevas
Alejandro
A
Pérez-Rey
David
D
Martín
Luis
L
Anguita
Alberto
A
de la Iglesia
Diana
D
de la Calle
Guillermo
G
Crespo
José
J
Maojo
Víctor
V
D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D020407:Internet; D009696:Nucleic Acids / Q000737:chemistry*; D039781:PubMed; D012984:Software
D009696:Nucleic Acids