GenArk : towards a million UCSC genome browsers
© 2023. BioMed Central Ltd., part of Springer Nature..
Interactive graphical genome browsers are essential tools in genomics, but they do not contain all the recent genome assemblies. We create Genome Archive (GenArk) collection of UCSC Genome Browsers from NCBI assemblies. Built on our established track hub system, this enables fast visualization of annotations. Assemblies come with gene models, repeat masks, BLAT, and in silico PCR. Users can add annotations via track hubs and custom tracks. We can bulk-import third-party resources, demonstrated with TOGA and Ensembl gene models for hundreds of assemblies.Three thousand two hundred sixty-nine GenArk assemblies are listed at https://hgdownload.soe.ucsc.edu/hubs/ and can be searched for on the Genome Browser gateway page.
| Errataetall: | |
|---|---|
| Medienart: |
E-Artikel |
| Erscheinungsjahr: |
2023 |
|---|---|
| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:24 |
|---|---|
| Enthalten in: |
Genome biology - 24(2023), 1 vom: 02. Okt., Seite 217 |
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
Clawson, Hiram [VerfasserIn] |
|---|
| Links: |
|---|
| Themen: |
Journal Article |
|---|
| Anmerkungen: |
Date Completed 04.10.2023 Date Revised 25.04.2024 published: Electronic UpdateOf: Res Sq. 2023 Apr 03;:. - PMID 37066427 Citation Status MEDLINE |
|---|
| doi: |
10.1186/s13059-023-03057-x |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
NLM362799490 |
|---|
| LEADER | 01000caa a22002652 4500 | ||
|---|---|---|---|
| 001 | NLM362799490 | ||
| 003 | DE-627 | ||
| 005 | 20240425232404.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 231226s2023 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1186/s13059-023-03057-x |2 doi | |
| 028 | 5 | 2 | |a pubmed24n1386.xml |
| 035 | |a (DE-627)NLM362799490 | ||
| 035 | |a (NLM)37784172 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 100 | 1 | |a Clawson, Hiram |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a GenArk |b towards a million UCSC genome browsers |
| 264 | 1 | |c 2023 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a ƒaComputermedien |b c |2 rdamedia | ||
| 338 | |a ƒa Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Date Completed 04.10.2023 | ||
| 500 | |a Date Revised 25.04.2024 | ||
| 500 | |a published: Electronic | ||
| 500 | |a UpdateOf: Res Sq. 2023 Apr 03;:. - PMID 37066427 | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a © 2023. BioMed Central Ltd., part of Springer Nature. | ||
| 520 | |a Interactive graphical genome browsers are essential tools in genomics, but they do not contain all the recent genome assemblies. We create Genome Archive (GenArk) collection of UCSC Genome Browsers from NCBI assemblies. Built on our established track hub system, this enables fast visualization of annotations. Assemblies come with gene models, repeat masks, BLAT, and in silico PCR. Users can add annotations via track hubs and custom tracks. We can bulk-import third-party resources, demonstrated with TOGA and Ensembl gene models for hundreds of assemblies.Three thousand two hundred sixty-nine GenArk assemblies are listed at https://hgdownload.soe.ucsc.edu/hubs/ and can be searched for on the Genome Browser gateway page | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Research Support, Non-U.S. Gov't | |
| 650 | 4 | |a Research Support, N.I.H., Extramural | |
| 700 | 1 | |a Lee, Brian T |e verfasserin |4 aut | |
| 700 | 1 | |a Raney, Brian J |e verfasserin |4 aut | |
| 700 | 1 | |a Barber, Galt P |e verfasserin |4 aut | |
| 700 | 1 | |a Casper, Jonathan |e verfasserin |4 aut | |
| 700 | 1 | |a Diekhans, Mark |e verfasserin |4 aut | |
| 700 | 1 | |a Fischer, Clay |e verfasserin |4 aut | |
| 700 | 1 | |a Gonzalez, Jairo Navarro |e verfasserin |4 aut | |
| 700 | 1 | |a Hinrichs, Angie S |e verfasserin |4 aut | |
| 700 | 1 | |a Lee, Christopher M |e verfasserin |4 aut | |
| 700 | 1 | |a Nassar, Luis R |e verfasserin |4 aut | |
| 700 | 1 | |a Perez, Gerardo |e verfasserin |4 aut | |
| 700 | 1 | |a Wick, Brittney |e verfasserin |4 aut | |
| 700 | 1 | |a Schmelter, Daniel |e verfasserin |4 aut | |
| 700 | 1 | |a Speir, Matthew L |e verfasserin |4 aut | |
| 700 | 1 | |a Armstrong, Joel |e verfasserin |4 aut | |
| 700 | 1 | |a Zweig, Ann S |e verfasserin |4 aut | |
| 700 | 1 | |a Kuhn, Robert M |e verfasserin |4 aut | |
| 700 | 1 | |a Kirilenko, Bogdan M |e verfasserin |4 aut | |
| 700 | 1 | |a Hiller, Michael |e verfasserin |4 aut | |
| 700 | 1 | |a Haussler, David |e verfasserin |4 aut | |
| 700 | 1 | |a Kent, W James |e verfasserin |4 aut | |
| 700 | 1 | |a Haeussler, Maximilian |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Genome biology |d 2000 |g 24(2023), 1 vom: 02. Okt., Seite 217 |w (DE-627)NLM110197372 |x 1474-760X |7 nnns |
| 773 | 1 | 8 | |g volume:24 |g year:2023 |g number:1 |g day:02 |g month:10 |g pages:217 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.1186/s13059-023-03057-x |3 Volltext |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a GBV_NLM | ||
| 951 | |a AR | ||
| 952 | |d 24 |j 2023 |e 1 |b 02 |c 10 |h 217 | ||