Update in Gynecology and Obstetrics: reviews and databases

There is a considerable body of new information on Gynecology and Obstetrics. To aid in keeping gynecologists updated, renowned periodicals publish review articles. Review articles enable the reader to obtain the best evidence for clinical or research issues from several individual articles. This enables the professional to make clinical decisions in the light of current knowledge. The different types of reviews and database that may be used for the elaboration of reviews are discussed in the present article. It is suggested that future reviews on Gynecology and Obstetrics include articles published in other idioms apart from English and that a larger number of database is researched. Thus, reviews will be not only more inclusive but more representative of the international literature.

Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data

Motivation: DNA assembly programs classically perform an all-against-all comparison of reads to identify overlaps, followed by a multiple sequence alignment and generation of a consensus sequence. If the aim is to assemble a particular segment, instead of a whole genome or transcriptome, a target-specific assembly is a more sensible approach. GenSeed is a Perl program that implements a seed-driven recursive assembly consisting of cycles comprising a similarity search, read selection and assembly. The iterative process results in a progressive extension of the original seed sequence. GenSeed was tested and validated on many applications, including the reconstruction of nuclear genes or segments, full-length transcripts, and extrachromosomal genomes. The robustness of the method was confirmed through the use of a variety of DNA and protein seeds, including short sequences derived from SAGE and proteome projects.