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» An analysis framework for search sequences
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NAR
2007
124views more  NAR 2007»
15 years 5 months ago
EVEREST: a collection of evolutionary conserved protein domains
Protein domains are subunits of proteins that recur throughout the protein world. There are many definitions attempting to capture the essence of a protein domain, and several sys...
Elon Portugaly, Nathan Linial, Michal Linial
BMCBI
2007
133views more  BMCBI 2007»
15 years 6 months ago
MATLIGN: a motif clustering, comparison and matching tool
Background: Sequence motifs representing transcription factor binding sites (TFBS) are commonly encoded as position frequency matrices (PFM) or degenerate consensus sequences (CS)...
Matti Kankainen, Ari Löytynoja
BMCBI
2007
115views more  BMCBI 2007»
15 years 6 months ago
Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites
Background: We performed an exhaustive search for local structural similarities in an ensemble of non-redundant protein functional sites. With the purpose of finding new examples ...
Gabriele Ausiello, Daniele Peluso, Allegra Via, Ma...
BMCBI
2002
126views more  BMCBI 2002»
15 years 6 months ago
RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs
Background: When analyzing protein sequences using sequence similarity searches, orthologous sequences (that diverged by speciation) are more reliable predictors of a new protein&...
Christian M. Zmasek, Sean R. Eddy
WWW
2005
ACM
16 years 7 months ago
Ranking a stream of news
According to a recent survey made by Nielsen NetRatings, searching on news articles is one of the most important activity online. Indeed, Google, Yahoo, MSN and many others have p...
Gianna M. Del Corso, Antonio Gulli, Francesco Roma...