Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures

A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives

(2011) Julie D. Thompson et al.   PLoS One

Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud

(2010) P. Di Tommaso et al.   BIOINFORMATICS

T-RMSD: A Fine-grained, Structure-based Classification Method and its Application to the Functional Characterization of TNF Receptors

(2010) Cedrik Magis et al.   JOURNAL OF MOLECULAR BIOLOGY

The RCSB Protein Data Bank: redesigned web site and web services

(2010) P. W. Rose et al.   NUCLEIC ACIDS RESEARCH

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

Upcoming challenges for multiple sequence alignment methods in the high-throughput era

(2009) Carsten Kemena et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Structure-Based Prediction of the Saccharomyces cerevisiae SH3–Ligand Interactions

(2009) Gregorio Fernandez-Ballester et al.   JOURNAL OF MOLECULAR BIOLOGY

PhyloWidget: web-based visualizations for the tree of life

(2008) G. E. Jordan et al.   BIOINFORMATICS

RNAalifold: improved consensus structure prediction for RNA alignments

(2008) Stephan H Bernhart et al.   BMC BIOINFORMATICS

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

R-Coffee: a method for multiple alignment of non-coding RNA

(2008) A. Wilm et al.   NUCLEIC ACIDS RESEARCH

PROMALS3D: a tool for multiple protein sequence and structure alignments

(2008) Jimin Pei et al.   NUCLEIC ACIDS RESEARCH

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

Rfam: updates to the RNA families database

(2008) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

Analysis and classification of RNA tertiary structures

(2008) M. Abraham et al.   RNA

Alignment Uncertainty and Genomic Analysis

(2008) K. M. Wong et al.   SCIENCE