Rapid similarity search of proteins using alignments of domain arrangements

Domain enhanced lookup time accelerated BLAST

(2012) Grzegorz M Boratyn et al.   Biology Direct

Ortholog identification in the presence of domain architecture rearrangement

(2011) K. Sjolander et al.   BRIEFINGS IN BIOINFORMATICS

InterPro in 2011: new developments in the family and domain prediction database

(2011) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

Reorganizing the protein space at the Universal Protein Resource (UniProt)

(2011)   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Hidden Markov model speed heuristic and iterative HMM search procedure

(2010) L Steven Johnson et al.   BMC BIOINFORMATICS

Homologous over-extension: a challenge for iterative similarity searches

(2010) Mileidy W. Gonzalez et al.   NUCLEIC ACIDS RESEARCH

OMA 2011: orthology inference among 1000 complete genomes

(2010) A. M. Altenhoff et al.   NUCLEIC ACIDS RESEARCH

Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species

(2010) J. H. Werren et al.   SCIENCE

Quantifying the mechanisms of domain gain in animal proteins

(2010) Marija Buljan et al.   GENOME BIOLOGY

Genomic and structural aspects of protein evolution

(2009) Cyrus Chothia et al.   BIOCHEMICAL JOURNAL

Detection of new protein domains using co-occurrence: application to Plasmodium falciparum

(2009) Nicolas Terrapon et al.   BIOINFORMATICS

Protein comparison at the domain architecture level

(2009) Byungwook Lee et al.   BMC BIOINFORMATICS

Protein domain organisation: adding order

(2009) Sarah K Kummerfeld et al.   BMC BIOINFORMATICS

The Evolutionary Mechanics of Domain Organization in Proteomes and the Rise of Modularity in the Protein World

(2009) Minglei Wang et al.   STRUCTURE

DAhunter: a web-based server that identifies homologous proteins by comparing domain architecture

(2008) B. Lee et al.   NUCLEIC ACIDS RESEARCH

Arrangements in the modular evolution of proteins

(2008) Andrew D. Moore et al.   TRENDS IN BIOCHEMICAL SCIENCES

Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins

(2008) Nan Song et al.   PLoS Computational Biology