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

Issues in bioinformatics benchmarking: the case study of multiple sequence alignment

(2010) M. R. Aniba et al.   NUCLEIC ACIDS RESEARCH

Multi-Harmony: detecting functional specificity from sequence alignment

(2010) B. W. Brandt et al.   NUCLEIC ACIDS RESEARCH

Protein interactions and ligand binding: From protein subfamilies to functional specificity

(2010) A. Rausell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

More Than 1,001 Problems with Protein Domain Databases: Transmembrane Regions, Signal Peptides and the Issue of Sequence Homology

(2010) Wing-Cheong Wong et al.   PLoS Computational Biology

Phylogenetic assessment of alignments reveals neglected tree signal in gaps

(2010) Christophe Dessimoz et al.   GENOME BIOLOGY

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Establishment of a Dog Model for the p53 Family Pathway and Identification of a Novel Isoform of p21 Cyclin-Dependent Kinase Inhibitor

(2009) Jin Zhang et al.   MOLECULAR CANCER RESEARCH

Darwinian evolution in the light of genomics

(2009) E. V. Koonin   NUCLEIC ACIDS RESEARCH

Evaluation of Three Automated Genome Annotations for Halorhabdus utahensis

(2009) Peter Bakke et al.   PLoS One

DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment

(2008) Amarendran R Subramanian et al.   Algorithms for Molecular Biology

INTREPID—INformation-theoretic TREe traversal for Protein functional site IDentification

(2008) Sriram Sankararaman et al.   BIOINFORMATICS

A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences

(2008) Claudia Chica et al.   BMC BIOINFORMATICS

Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species

(2008) Oliver Keller et al.   BMC BIOINFORMATICS

Recent developments in the MAFFT multiple sequence alignment program

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

Sonic hedgehog mutations identified in holoprosencephaly patients can act in a dominant negative manner

(2008) Samer Singh et al.   HUMAN GENETICS

Species-level diversification of African dwarf crocodiles (Genus Osteolaemus): A geographic and phylogenetic perspective

(2008) Mitchell J. Eaton et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features

(2008) Timo Lassmann et al.   NUCLEIC ACIDS RESEARCH

Alignment Uncertainty and Genomic Analysis

(2008) K. M. Wong et al.   SCIENCE

The Eukaryotic Genome as an RNA Machine

(2008) P. P. Amaral et al.   SCIENCE

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE

The impact of next-generation sequencing technology on genetics

(2008) Elaine R. Mardis   TRENDS IN GENETICS

Bioinformatics challenges of new sequencing technology

(2008) Mihai Pop et al.   TRENDS IN GENETICS