Canis mtDNA HV1 database: a web-based tool for collecting and surveying Canis mtDNA HV1 haplotype in public database
Abstract Background Canine and wolf mitochondrial DNA haplotypes, which can be used for forensic or phylogenetic analyses, have been defined in various schemes depending on the region analyzed. In recent studies, the 582 bp fragment of the HV1 region is most commonly used. 317 different canine HV1 h...
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ftdoajarticles:oai:doaj.org/article:f6b8dcad317e483ab84938950f176239 2023-05-15T15:50:07+02:00 Canis mtDNA HV1 database: a web-based tool for collecting and surveying Canis mtDNA HV1 haplotype in public database Quan Ke Thai Dung Anh Chung Hoang-Dung Tran 2017-06-01T00:00:00Z https://doi.org/10.1186/s12863-017-0528-0 https://doaj.org/article/f6b8dcad317e483ab84938950f176239 EN eng BMC http://link.springer.com/article/10.1186/s12863-017-0528-0 https://doaj.org/toc/1471-2156 doi:10.1186/s12863-017-0528-0 1471-2156 https://doaj.org/article/f6b8dcad317e483ab84938950f176239 BMC Genetics, Vol 18, Iss 1, Pp 1-7 (2017) Control region Canis lupus familiaris Database Haplotype identifier HV1 haplotype Genetics QH426-470 article 2017 ftdoajarticles https://doi.org/10.1186/s12863-017-0528-0 2022-12-30T23:25:13Z Abstract Background Canine and wolf mitochondrial DNA haplotypes, which can be used for forensic or phylogenetic analyses, have been defined in various schemes depending on the region analyzed. In recent studies, the 582 bp fragment of the HV1 region is most commonly used. 317 different canine HV1 haplotypes have been reported in the rapidly growing public database GenBank. These reported haplotypes contain several inconsistencies in their haplotype information. To overcome this issue, we have developed a Canis mtDNA HV1 database. This database collects data on the HV1 582 bp region in dog mitochondrial DNA from the GenBank to screen and correct the inconsistencies. It also supports users in detection of new novel mutation profiles and assignment of new haplotypes. Description The Canis mtDNA HV1 database (CHD) contains 5567 nucleotide entries originating from 15 subspecies in the species Canis lupus. Of these entries, 3646 were haplotypes and grouped into 804 distinct sequences. 319 sequences were recognized as previously assigned haplotypes, while the remaining 485 sequences had new mutation profiles and were marked as new haplotype candidates awaiting further analysis for haplotype assignment. Of the 3646 nucleotide entries, only 414 were annotated with correct haplotype information, while 3232 had insufficient or lacked haplotype information and were corrected or modified before storing in the CHD. The CHD can be accessed at http://chd.vnbiology.com . It provides sequences, haplotype information, and a web-based tool for mtDNA HV1 haplotyping. The CHD is updated monthly and supplies all data for download. Conclusions The Canis mtDNA HV1 database contains information about canine mitochondrial DNA HV1 sequences with reconciled annotation. It serves as a tool for detection of inconsistencies in GenBank and helps identifying new HV1 haplotypes. Thus, it supports the scientific community in naming new HV1 haplotypes and to reconcile existing annotation of HV1 582 bp sequences. Article in Journal/Newspaper Canis lupus Directory of Open Access Journals: DOAJ Articles BMC Genetics 18 1 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Control region Canis lupus familiaris Database Haplotype identifier HV1 haplotype Genetics QH426-470 |
spellingShingle |
Control region Canis lupus familiaris Database Haplotype identifier HV1 haplotype Genetics QH426-470 Quan Ke Thai Dung Anh Chung Hoang-Dung Tran Canis mtDNA HV1 database: a web-based tool for collecting and surveying Canis mtDNA HV1 haplotype in public database |
topic_facet |
Control region Canis lupus familiaris Database Haplotype identifier HV1 haplotype Genetics QH426-470 |
description |
Abstract Background Canine and wolf mitochondrial DNA haplotypes, which can be used for forensic or phylogenetic analyses, have been defined in various schemes depending on the region analyzed. In recent studies, the 582 bp fragment of the HV1 region is most commonly used. 317 different canine HV1 haplotypes have been reported in the rapidly growing public database GenBank. These reported haplotypes contain several inconsistencies in their haplotype information. To overcome this issue, we have developed a Canis mtDNA HV1 database. This database collects data on the HV1 582 bp region in dog mitochondrial DNA from the GenBank to screen and correct the inconsistencies. It also supports users in detection of new novel mutation profiles and assignment of new haplotypes. Description The Canis mtDNA HV1 database (CHD) contains 5567 nucleotide entries originating from 15 subspecies in the species Canis lupus. Of these entries, 3646 were haplotypes and grouped into 804 distinct sequences. 319 sequences were recognized as previously assigned haplotypes, while the remaining 485 sequences had new mutation profiles and were marked as new haplotype candidates awaiting further analysis for haplotype assignment. Of the 3646 nucleotide entries, only 414 were annotated with correct haplotype information, while 3232 had insufficient or lacked haplotype information and were corrected or modified before storing in the CHD. The CHD can be accessed at http://chd.vnbiology.com . It provides sequences, haplotype information, and a web-based tool for mtDNA HV1 haplotyping. The CHD is updated monthly and supplies all data for download. Conclusions The Canis mtDNA HV1 database contains information about canine mitochondrial DNA HV1 sequences with reconciled annotation. It serves as a tool for detection of inconsistencies in GenBank and helps identifying new HV1 haplotypes. Thus, it supports the scientific community in naming new HV1 haplotypes and to reconcile existing annotation of HV1 582 bp sequences. |
format |
Article in Journal/Newspaper |
author |
Quan Ke Thai Dung Anh Chung Hoang-Dung Tran |
author_facet |
Quan Ke Thai Dung Anh Chung Hoang-Dung Tran |
author_sort |
Quan Ke Thai |
title |
Canis mtDNA HV1 database: a web-based tool for collecting and surveying Canis mtDNA HV1 haplotype in public database |
title_short |
Canis mtDNA HV1 database: a web-based tool for collecting and surveying Canis mtDNA HV1 haplotype in public database |
title_full |
Canis mtDNA HV1 database: a web-based tool for collecting and surveying Canis mtDNA HV1 haplotype in public database |
title_fullStr |
Canis mtDNA HV1 database: a web-based tool for collecting and surveying Canis mtDNA HV1 haplotype in public database |
title_full_unstemmed |
Canis mtDNA HV1 database: a web-based tool for collecting and surveying Canis mtDNA HV1 haplotype in public database |
title_sort |
canis mtdna hv1 database: a web-based tool for collecting and surveying canis mtdna hv1 haplotype in public database |
publisher |
BMC |
publishDate |
2017 |
url |
https://doi.org/10.1186/s12863-017-0528-0 https://doaj.org/article/f6b8dcad317e483ab84938950f176239 |
genre |
Canis lupus |
genre_facet |
Canis lupus |
op_source |
BMC Genetics, Vol 18, Iss 1, Pp 1-7 (2017) |
op_relation |
http://link.springer.com/article/10.1186/s12863-017-0528-0 https://doaj.org/toc/1471-2156 doi:10.1186/s12863-017-0528-0 1471-2156 https://doaj.org/article/f6b8dcad317e483ab84938950f176239 |
op_doi |
https://doi.org/10.1186/s12863-017-0528-0 |
container_title |
BMC Genetics |
container_volume |
18 |
container_issue |
1 |
_version_ |
1766385104200925184 |