A web tool for comparative genomics: G-compass

Fujii, Yasuyuki; Itoh, Takeshi; Sakate, Ryuichi; Koyanagi, Kanako O.; Matsuya, Akihiro; Habara, Takuya; Yamaguchi, Kaori; Kaneko, Yayoi; Gojobori, Takashi; Imanishi, Tadashi

doi:10.1016/j.gene.2005.05.043

Cited by 6 publications

(7 citation statements)

References 25 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In this study, the human-chimpanzee alignments were generated by the G-compass pipeline [12]. Although the G-compass pipeline is different from the UCSC axtNet alignment [16] based on the definition of orthologous alignments, both methods initially generate local alignments with blastz [16] or its successor lastz [17].…”

Section: Discussionmentioning

confidence: 99%

“…The alignments were constructed with the G-compass pipeline [11,12] based on the blastz local alignments [16] and its unique and non-redundant reciprocal best hits. Applying the method above after setting p d and p g at 0.0136 and 0.00150 respectively, we obtained ultramicro inversions within the human-chimpanzee alignments.…”

Section: Methodsmentioning

confidence: 99%

“…In order to examine the impact of ultramicro inversions on the genome alignment, we developed a method for identifying ultramicro inversions within the alignments between the human and chimpanzee genomes. We first generated 2.41 Gb of one-to-one (i.e., orthologous) alignments between the human and chimpanzee genomes using the G-compass pipeline [11,12], and identified inversions in each local alignment. Subsequently, we examined the relationships of ultramicro inversions with the structural features of the human genome to determine the molecular mechanisms of the inversions.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Abundance of ultramicro inversions within local alignments between human and chimpanzee genomes

Hara

Imanishi

2011

BMC Evol Biol

Self Cite

View full text Add to dashboard Cite

BackgroundChromosomal inversion is one of the most important mechanisms of evolution. Recent studies of comparative genomics have revealed that chromosomal inversions are abundant in the human genome. While such previously characterized inversions are large enough to be identified as a single alignment or a string of local alignments, the impact of ultramicro inversions, which are such short that the local alignments completely cover them, on evolution is still uncertain.ResultsIn this study, we developed a method for identifying ultramicro inversions by scanning of local alignments. This technique achieved a high sensitivity and a very low rate of false positives. We identified 2,377 ultramicro inversions ranging from five to 125 bp within the orthologous alignments between the human and chimpanzee genomes. The false positive rate was estimated to be around 4%. Based on phylogenetic profiles using the primate outgroups, 479 ultramicro inversions were inferred to have specifically inverted in the human lineage. Ultramicro inversions exclusively involving adenine and thymine were the most frequent; 461 inversions (19.4%) of the total. Furthermore, the density of ultramicro inversions in chromosome Y and the neighborhoods of transposable elements was higher than average. Sixty-five ultramicro inversions were identified within the exons of human protein-coding genes.ConclusionsWe defined ultramicro inversions as the inverted regions equal to or smaller than 125 bp buried within local alignments. Our observations suggest that ultramicro inversions are abundant among the human and chimpanzee genomes, and that location of the inversions correlated with the genome structural instability. Some of the ultramicro inversions may contribute to gene evolution. Our inversion-identification method is also applicable in the fine-tuning of genome alignments by distinguishing ultramicro inversions from nucleotide substitutions and indels.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Abundance of ultramicro inversions within local alignments between human and chimpanzee genomes

Hara

Imanishi

2011

BMC Evol Biol

Self Cite

View full text Add to dashboard Cite

show abstract

“…Orthologous alignments among the four species were constructed based on two procedures as described later. Orthologous pairwise alignments between the human and each great ape sequences were generated with the G-compass pipeline (Fujii et al 2005; Kawahara et al 2009) based on LASTZ local alignments (Harris 2007) and its unique and nonredundant reciprocal best hits. Subsequently, the human genomic regions that possessed the orthologous pairwise alignments to all the three great ape were extracted and multiply re-aligned with the corresponding sequences of the three apes with MAFFT (Katoh and Toh 2008).…”

Section: Methodsmentioning

confidence: 99%

Reconstructing the Demographic History of the Human Lineage Using Whole-Genome Sequences from Human and Three Great Apes

Hara

Imanishi

Satta

2012

Genome Biology and Evolution

Self Cite

View full text Add to dashboard Cite

The demographic history of human would provide helpful information for identifying the evolutionary events that shaped the humanity but remains controversial even in the genomic era. To settle the controversies, we inferred the speciation times (T) and ancestral population sizes (N) in the lineage leading to human and great apes based on whole-genome alignment. A coalescence simulation determined the sizes of alignment blocks and intervals between them required to obtain recombination-free blocks with a high frequency. This simulation revealed that the size of the block strongly affects the parameter inference, indicating that recombination is an important factor for achieving optimum parameter inference. From the whole genome alignments (1.9 giga-bases) of human (H), chimpanzee (C), gorilla (G), and orangutan, 100-bp alignment blocks separated by ≥5-kb intervals were sampled and subjected to estimate τ = μT and θ = 4μgN using the Markov chain Monte Carlo method, where μ is the mutation rate and g is the generation time. Although the estimated τHC differed across chromosomes, τHC and τHCG were strongly correlated across chromosomes, indicating that variation in τ is subject to variation in μ, rather than T, and thus, all chromosomes share a single speciation time. Subsequently, we estimated Ts of the human lineage from chimpanzee, gorilla, and orangutan to be 6.0–7.6, 7.6–9.7, and 15–19 Ma, respectively, assuming variable μ across lineages and chromosomes. These speciation times were consistent with the fossil records. We conclude that the speciation times in our recombination-free analysis would be conclusive and the speciation between human and chimpanzee was a single event.

show abstract

“…However, these browsers were designed to consider one genome as a reference, showing the patterns of genomic conservation of other genomes along the reference genome. The previous version of G-compass (Fujii et al ., 2005), which only provided human–mouse genome comparisons, also considered the human genome as a reference. These browsers do not provide a quick overview of the genomic conservations and synteny information simultaneously in parallel.…”

Section: Introductionmentioning

confidence: 99%

G-compass: a web-based comparative genome browser between human and other vertebrate genomes

et al. 2009

View full text Add to dashboard Cite

Summary: G-compass is designed for efficient comparative genome analysis between human and other vertebrate genomes. The current version of G-compass allows us to browse two corresponding genomic regions between human and another species in parallel. One-to-one evolutionarily conserved regions (i.e. orthologous regions) between species are highlighted along the genomes. Information such as locations of duplicated regions, copy number variations and mammalian ultra-conserved elements is also provided. These features of G-compass enable us to easily determine patterns of genomic rearrangements and changes in gene orders through evolutionary time. Since G-compass is a satellite database of H-InvDB, which is a comprehensive annotation resource for human genes and transcripts, users can easily refer to manually curated functional annotations and other abundant biological information for each human transcript. G-compass is expected to be a valuable tool for comparing human and model organisms and promoting the exchange of functional information.Availability: G-compass is freely available at http://www.h-invitational.jp/g-compass/.Contact: t.imanishi@aist.go.jp

show abstract

A web tool for comparative genomics: G-compass

Cited by 6 publications

References 25 publications

Abundance of ultramicro inversions within local alignments between human and chimpanzee genomes

Abundance of ultramicro inversions within local alignments between human and chimpanzee genomes

Reconstructing the Demographic History of the Human Lineage Using Whole-Genome Sequences from Human and Three Great Apes

G-compass: a web-based comparative genome browser between human and other vertebrate genomes

Contact Info

Product

Resources

About