Published in Bioinformatics on August 31, 2013
A simple method to control over-alignment in the MAFFT multiple sequence alignment program. Bioinformatics (2016) 1.05
The Dfam database of repetitive DNA families. Nucleic Acids Res (2015) 0.91
Most partial domains in proteins are alignment and annotation artifacts. Genome Biol (2015) 0.85
Parameterizing sequence alignment with an explicit evolutionary model. BMC Bioinformatics (2015) 0.81
Finding Protein and Nucleotide Similarities with FASTA. Curr Protoc Bioinformatics (2016) 0.81
Query-seeded iterative sequence similarity searching improves selectivity 5-20-fold. Nucleic Acids Res (2016) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A (1992) 61.33
BLAST+: architecture and applications. BMC Bioinformatics (2009) 36.53
The Pfam protein families database. Nucleic Acids Res (2011) 33.46
Amino acid substitution matrices from an information theoretic perspective. J Mol Biol (1991) 23.38
Flexible sequence similarity searching with the FASTA3 program package. Methods Mol Biol (2000) 12.05
Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc Natl Acad Sci U S A (1998) 7.18
Estimating amino acid substitution models: a comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method. Mol Biol Evol (2002) 7.03
Comparison of methods for searching protein sequence databases. Protein Sci (1995) 4.29
Empirical determination of effective gap penalties for sequence comparison. Bioinformatics (2002) 1.78
Homologous over-extension: a challenge for iterative similarity searches. Nucleic Acids Res (2010) 1.70
The limits of protein sequence comparison? Curr Opin Struct Biol (2005) 1.57
A new approach to sequence comparison: normalized sequence alignment. Bioinformatics (2001) 1.33
Locating well-conserved regions within a pairwise alignment. Comput Appl Biosci (1993) 1.16
RefProtDom: a protein database with improved domain boundaries and homology relationships. Bioinformatics (2010) 0.96
The genome of Cryptosporidium hominis. Nature (2004) 3.93
Sensitivity and selectivity in protein structure comparison. Protein Sci (2004) 3.69
Homologous over-extension: a challenge for iterative similarity searches. Nucleic Acids Res (2010) 1.70
Getting more from less: algorithms for rapid protein identification with multiple short peptide sequences. Mol Cell Proteomics (2002) 1.70
MACiE: exploring the diversity of biochemical reactions. Nucleic Acids Res (2011) 1.67
The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. Nucleic Acids Res (2013) 1.42
Nomenclature for mammalian soluble glutathione transferases. Methods Enzymol (2005) 1.36
Identification of residues in glutathione transferase capable of driving functional diversification in evolution. A novel approach to protein redesign. J Biol Chem (2002) 1.15
PSI-Search: iterative HOE-reduced profile SSEARCH searching. Bioinformatics (2012) 1.14
A strategy for the rapid identification of phosphorylation sites in the phosphoproteome. Mol Cell Proteomics (2002) 0.97
RefProtDom: a protein database with improved domain boundaries and homology relationships. Bioinformatics (2010) 0.96
Entamoeba histolytica: sequence conservation of the Gal/GalNAc lectin from clinical isolates. Exp Parasitol (2002) 0.93
Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments. BMC Bioinformatics (2010) 0.88
Globally, unrelated protein sequences appear random. Bioinformatics (2009) 0.82
CRP: Cleavage of Radiolabeled Phosphoproteins. Nucleic Acids Res (2003) 0.80
Identification and characterization of GSTT3, a third murine Theta class glutathione transferase. Biochem J (2002) 0.80
Visualization of near-optimal sequence alignments. Bioinformatics (2004) 0.79
Using relational databases for improved sequence similarity searching and large-scale genomic analyses. Curr Protoc Bioinformatics (2004) 0.75