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» Genome Alignments Using MPI-LAGAN
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BMCBI
2007
152views more  BMCBI 2007»
13 years 7 months ago
A cross-species alignment tool (CAT)
Background: The main two sorts of automatic gene annotation frameworks are ab initio and alignment-based, the latter splitting into two sub-groups. The first group is used for int...
Heng Li, Liang Guan, Tao Liu, Yiran Guo, Wei-Mou Z...
BMCBI
2006
108views more  BMCBI 2006»
13 years 7 months ago
RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits
Background: Until today, analysis of 16S ribosomal RNA (rRNA) sequences has been the de-facto gold standard for the assessment of phylogenetic relationships among prokaryotes. How...
Hanno Teeling, Frank Oliver Glöckner
NAR
2011
198views Computer Vision» more  NAR 2011»
12 years 10 months ago
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralo
The growing availability of complete genomic sequences from diverse species has brought about the need to scale up phylogenomic analyses, including the reconstruction of large col...
Jaime Huerta-Cepas, Salvador Capella-Gutiér...
BMCBI
2006
103views more  BMCBI 2006»
13 years 7 months ago
Cis-motifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequili
Background: The discovery of cis-regulatory motifs still remains a challenging task even though the number of sequenced genomes is constantly growing. Computational analyses using...
Kenneth W. Berendzen, Kurt Stüber, Klaus Hart...
CSB
2003
IEEE
110views Bioinformatics» more  CSB 2003»
14 years 24 days ago
Prokaryote Phylogeny without Sequence Alignment: From Avoidance Signature to Composition Distance
A new and essentially simple method to reconstruct prokaryotic phylogenetic trees from their complete genome data without using sequence alignment is proposed. It is based on the ...
Bailin Hao, Ji Qi