Hvr Base is a platform providing resources and tools related to bioinformatics and molecular biology.
Welcome to the HvrBase site
The HvrBase was developed as a tool to facilitate the retrieval and analysis of human and primate mitochondrial DNA (mtDNA).
Introduction
We present here the mtDNA collection originally mentioned in Compilation of human mtDNA control region sequences. See also the update HvrBase: Compilation of mtDNA control region sequences from primates.
HvrBase is a compilation of human and ape mtDNA control region sequences. Sequences and related informations on individuals, such as from where the sequences were obtained, is stored in a relational database. The HvrBase is via www available from everywhere in the world.
Data on Mitochondrial Hypervariable Regions:
The site also compiles and provides access to sequences from the hypervariable regions (HVRI and HVRII) of human mitochondrial DNA. This resource is valuable for researchers in genetics and evolutionary studies.
Tools like AxonTracker:
This software is designed for tracking and labeling axon structures in motor axon connectome datasets. It's a freeware developed by the Center for Bioengineering and Informatics in collaboration with Harvard's Department of Molecular and Cellular Biology. It is user-friendly, providing both 2D and 3D views of datasets.
Compilation of human mtDNA control region sequences
The history of human populations is studied for a wealth of different genetic systems. Because the mitochondrial genome is maternally inherited and accumulates substitutions at a higher rate than the nuclear genome, it is well suited to analyse the population history of humans based on simple models of
population history. Especially the hypervariable regions HVRI and HVRII of the control region have been studied extensively. Since 1981 the amount of available HVRI and HVRII data has increased exponentially (Fig. 1). We have collected and aligned a large number of control-region sequences. This paper describes the organisation of the database.
COMPILATION OF SEQUENCES
Sequences were collected from publications or were retrieved from GenBank and stored as plain ASCII files. Sequences from GenBank were compared to the sequences in the corresponding publications. If discrepancies occurred the sequences were stored as given in the paper. If only sequence positions deviating from the reference sequence were published these deviations were added to the reference sequence and the resulting sequence was stored. When the publication did not clearly state the start and end of a sequence, the first, respectively the last variable sites were used as limitation. Unfortunately, it was not always evident how often each lineage was found or to which population it belonged when individuals of more than one population were studied. If this could not be unraveled the data were not added to the collection. Sequences were manually aligned. For the HVRI region we aligned positions 16001–16408 and for the HVRII region positions 1–408 were aligned. If sequences were longer than this alignment, they were truncated to the corresponding sites, if they were shorter, question marks were introduced to achieve the length required by the alignment. All non-determined nucleotides within a sequence are also represented by question marks. A dash (–) indicates an insertion or deletion of a nucleotide.
DESCRIPTION OF THE COMPILATION
The current collection comprises 4079 HVRI, 969 HVRII, and 728 human sequences where HVRI and HVRII are known. This amounts to 2298 and 580 (database)-lineages for HVRI and HVRII, repectively. 539 lineages are found among individuals where both HVRI and HVRII have been determined. These numbers also include some unpublished sequences [K.Bauer, H.Geisert, M.Krings, M.Laan, A.Salem, A.Sajantila and S.Pääbo (1997), manuscript in preparation], that will be made available as soon as they are in press.
HvrBase: Compilation of mtDNA control region sequences from primates
Introduction
HvrBase is an updated and extended version of the compilation of human mtDNA control region sequences . It consists of a collection of aligned sequences from the hypervariable regions I and II (HVRI and HVRII) together with available information about the individuals (humans or apes) from whom the sequences were obtained. The compilation was created to simplify the coordination of collection, alignment and storage of the huge amount of D-loop sequence data and relevant information that has accumulated in the course of various population studies during the last 10 years (1,2 and references therein). The vast majority of previously determined HVRI and HVRII sequences were human sequences and were consequently the focus of the first version of the compilation. However, since the amount of available control region sequences from apes is steadily increasing, we have added available data from Pan troglodytes (common chimpanzee), Pan paniscus (pygmy chimpanzee), Gorilla gorilla (gorilla) and Pongo pygmaeus (orangutan) to HvrBase. Here we describe the status of the updated human data, the novel ape data and the changes necessary to include the ape data in HvrBase. We also introduce a new Mac/PC database application with a graphical user interface.
COMPILATION OF SEQUENCES AND ORGANIZATION OF THE DATA
We adopted the same strategy to collect and organize the new information about the sequences as expatiated in the previous compilation. New human sequences were collected from the publications. Sequences from great apes were taken from available publications. To accomodate for the fact that HvrBase now comprises information from different species, an additional category, S: , was introduced to allow retrieval of sequences from specie
DESCRIPTION OF THE COMPILATION
Alignment
The dot matrix program ‘dotter’ was used as a visual aid to produce a global alignment for the ape and human sequences. Figure 2 displays the dot plot of HVRI regions of two randomly selected modern humans, a modern human and a neanderthal, as well as the dot plots obtained when comparing a human to a common chimpanzee, pygmy chimpanzee, gorilla and orangutan, respectively. From this picture it is obvious that the alignment is not a major problem for HVRI. However, it is notable that the gorilla shows a large deletion in region 16162–16264 as already observed by Foran et al. Using the dot plots as guides to align the sequences, the complete collection was manually aligned.
Humans
The current collection of human data comprises 5846 HVRI sequences and 2302 HVRII sequences. From 2061 individuals, HVRI and HVRII were both sequenced. These numbers also include some unpublished sequences that will be made available once they are in press. Table 1 displays the populations, grouped according to continents, for which at least 20 individuals were sequenced. For some individuals, a population affiliation was not specified. These sequences could not be classified. However, the number of classified individuals outweighs the number of ungrouped individuals, with the exception of America. Note that the number of available HVRII sequences within a population is usually smaller than the available number of HVRI sequences.
Great Apes
For the first time HvrBase includes sequences from the neanderthal, chimpanzees, gorillas and orangutans. Table 2 gives an overview of the sequenced individuals. Again the number of HVRI sequences outweighs that of HVRII sequences. From P.troglodytes, 264 individual HVRI sequences were determined, whereas the gorilla HVRI and the orangutan HVRI are represented by 28 individuals and 3 individuals, respectively. For HVRII, a total of 13 sequences are collected in HvrBase.
