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NAR
2011
212views Computer Vision» more  NAR 2011»
8 years 2 months ago
Phospho.ELM: a database of phosphorylation sites - update 2011
The Phospho.ELM resource (http://phospho.elm.eu .org) is a relational database designed to store in vivo and in vitro phosphorylation data extracted from the scientific literature...
Holger Dinkel, Claudia Chica, Allegra Via, Cathryn...
BMCBI
2011
8 years 2 months ago
Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation
Background: The Smith-Waterman algorithm for local sequence alignment is more sensitive than heuristic methods for database searching, but also more time-consuming. The fastest ap...
Torbjørn Rognes
BMCBI
2011
8 years 2 months ago
Protein alignment algorithms with an efficient backtracking routine on multiple GPUs
Background: Pairwise sequence alignment methods are widely used in biological research. The increasing number of sequences is perceived as one of the upcoming challenges for seque...
Jacek Blazewicz, Wojciech Frohmberg, Michal Kierzy...
BMCBI
2011
8 years 2 months ago
A user-friendly web portal for T-Coffee on supercomputers
Background: Parallel T-Coffee (PTC) was the first parallel implementation of the T-Coffee multiple sequence alignment tool. It is based on MPI and RMA mechanisms. Its purpose is t...
Josep Rius Torrento, Fernando Cores, Francesc Sols...
NAR
2010
140views more  NAR 2010»
8 years 6 months ago
GUIDANCE: a web server for assessing alignment confidence scores
Evaluating the accuracy of multiple sequence alignment (MSA) is critical for virtually every comparative sequence analysis that uses an MSA as input. Here we present the GUIDANCE ...
Osnat Penn, Eyal Privman, Haim Ashkenazy, Giddy La...
ACL
2010
8 years 9 months ago
Learning Script Knowledge with Web Experiments
We describe a novel approach to unsupervised learning of the events that make up a script, along with constraints on their temporal ordering. We collect naturallanguage descriptio...
Michaela Regneri, Alexander Koller, Manfred Pinkal
JCB
2000
101views more  JCB 2000»
8 years 11 months ago
Evaluation Measures of Multiple Sequence Alignments
Multiple sequence alignments (MSAs) are frequently used in the study of families of protein sequences or DNA/RNA sequences. They are a fundamental tool for the understanding of th...
Gaston H. Gonnet, Chantal Korostensky, Steven A. B...
BMCBI
2004
77views more  BMCBI 2004»
8 years 11 months ago
A structural study for the optimisation of functional motifs encoded in protein sequences
Background: A large number of PROSITE patterns select false positives and/or miss known true positives. It is possible that
Allegra Via, Manuela Helmer-Citterich
BMCBI
2004
94views more  BMCBI 2004»
8 years 11 months ago
GASP: Gapped Ancestral Sequence Prediction for proteins
Background: The prediction of ancestral protein sequences from multiple sequence alignments is useful for many bioinformatics analyses. Predicting ancestral sequences is not a sim...
Richard J. Edwards, Denis C. Shields
BMCBI
2004
158views more  BMCBI 2004»
8 years 11 months ago
Improvement of alignment accuracy utilizing sequentially conserved motifs
Background: Multiple sequence alignment algorithms are very important tools in molecular biology today. Accurate alignment of proteins is central to several areas such as homology...
Saikat Chakrabarti, Nitin Bhardwaj, Prem A. Anand,...
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