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Select item 99528531.

How to use the Candida Genome Database

Marek S. Skrzypek, Jonathan Binkley, Gavin Sherlock

Methods Mol Biol. Author manuscript; available in PMC 2023 Feb 24.

Published in final edited form as: Methods Mol Biol. 2022; 2542: 55–69. doi: 10.1007/978-1-0716-2549-1_4

PMCID:: PMC9952853

Article PDF–1.5M

Select item 22389942.

FlyBase: integration and improvements to query tools

Robert J. Wilson, Joshua L. Goodman, Victor B. Strelets, The FlyBase Consortium

Nucleic Acids Res. 2008 Jan; 36(Database issue): D588–D593. Published online 2007 Dec 26. doi: 10.1093/nar/gkm930

PMCID:: PMC2238994

Article PDF–7.3M

Select item 87281533.

scAPAdb: a comprehensive database of alternative polyadenylation at single-cell resolution

Sheng Zhu, Qiwei Lian, Wenbin Ye, Wei Qin, Zhe Wu, Guoli Ji, Xiaohui Wu

Nucleic Acids Res. 2022 Jan 7; 50(D1): D365–D370. Published online 2021 Sep 11. doi: 10.1093/nar/gkab795

PMCID:: PMC8728153

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Using FlyBase to Find Functionally Related Drosophila Genes

Alix J. Rey, Helen Attrill, Steven J. Marygold, the FlyBase Consortium

Methods Mol Biol. Author manuscript; available in PMC 2018 Jun 12.

Published in final edited form as: Methods Mol Biol. 2018; 1757: 493–512. doi: 10.1007/978-1-4939-7737-6_16

PMCID:: PMC5996772

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Select item 81411235.

The Rhododendron Plant Genome Database (RPGD): a comprehensive online omics database for Rhododendron

Ningyawen Liu, Lu Zhang, Yanli Zhou, Mengling Tu, Zhenzhen Wu, Daping Gui, Yongpeng Ma, Jihua Wang, Chengjun Zhang

BMC Genomics. 2021; 22: 376. Published online 2021 May 22. doi: 10.1186/s12864-021-07704-0

PMCID:: PMC8141123

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Select item 98255556.

dbCAN-seq update: CAZyme gene clusters and substrates in microbiomes

Jinfang Zheng, Boyang Hu, Xinpeng Zhang, Qiwei Ge, Yuchen Yan, Jerry Akresi, Ved Piyush, Le Huang, Yanbin Yin

Nucleic Acids Res. 2023 Jan 6; 51(D1): D557–D563. Published online 2022 Nov 18. doi: 10.1093/nar/gkac1068

PMCID:: PMC9825555

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dbCAN-PUL: a database of experimentally characterized CAZyme gene clusters and their substrates

Catherine Ausland, Jinfang Zheng, Haidong Yi, Bowen Yang, Tang Li, Xuehuan Feng, Bo Zheng, Yanbin Yin

Nucleic Acids Res. 2021 Jan 8; 49(D1): D523–D528. Published online 2020 Sep 17. doi: 10.1093/nar/gkaa742

PMCID:: PMC7778981

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dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation

Le Huang, Han Zhang, Peizhi Wu, Sarah Entwistle, Xueqiong Li, Tanner Yohe, Haidong Yi, Zhenglu Yang, Yanbin Yin

Nucleic Acids Res. 2018 Jan 4; 46(Database issue): D516–D521. Published online 2017 Oct 9. doi: 10.1093/nar/gkx894

PMCID:: PMC5753378

Article PDF–254K

Select item 27902999.

New mutant phenotype data curation system in the Saccharomyces Genome Database

Maria C. Costanzo, Marek S. Skrzypek, Robert Nash, Edith Wong, Gail Binkley, Stacia R. Engel, Benjamin Hitz, Eurie L. Hong, J. Michael Cherry, the Saccharomyces Genome Database Project

Database (Oxford) 2009; 2009: bap001. Published online 2009 Mar 16. doi: 10.1093/database/bap001

PMCID:: PMC2790299

Article PDF–629K

Select item 396496910.

FlyBase 102—advanced approaches to interrogating FlyBase

Susan E. St. Pierre, Laura Ponting, Raymund Stefancsik, Peter McQuilton, the FlyBase Consortium

Nucleic Acids Res. 2014 Jan 1; 42(Database issue): D780–D788. Published online 2013 Nov 13. doi: 10.1093/nar/gkt1092

PMCID:: PMC3964969

Article PDF–16M

Select item 302638111.

PEPPI: a peptidomic database of human protein isoforms for proteomics experiments

Ao Zhou, Fan Zhang, Jake Y Chen

BMC Bioinformatics. 2010; 11(Suppl 6): S7. Published online 2010 Oct 7. doi: 10.1186/1471-2105-11-S6-S7

PMCID:: PMC3026381

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flyDIVaS: A Comparative Genomics Resource for Drosophila Divergence and Selection

Craig E. Stanley, Jr., Rob J. Kulathinal

G3 (Bethesda) 2016 Aug; 6(8): 2355–2363. Published online 2016 May 25. doi: 10.1534/g3.116.031138

PMCID:: PMC4978890

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Select item 268650713.

SysZNF: the C2H2 zinc finger gene database

Guohui Ding, Peter Lorenz, Michael Kreutzer, Yixue Li, Hans-Juergen Thiesen

Nucleic Acids Res. 2009 Jan; 37(Database issue): D267–D273. Published online 2008 Oct 30. doi: 10.1093/nar/gkn782

PMCID:: PMC2686507

Article PDF–6.8M

Select item 989879214.

ImmCellFie: A user-friendly web-based platform to infer metabolic function from omics data

Helen O. Masson, David Borland, Jason Reilly, Adrian Telleria, Shalki Shrivastava, Matt Watson, Luthfi Bustillos, Zerong Li, Laura Capps, Benjamin P. Kellman, Zachary A. King, Anne Richelle, Nathan E. Lewis, Kimberly Robasky

STAR Protoc. 2023 Mar 17; 4(1): 102069. Published online 2023 Jan 25. doi: 10.1016/j.xpro.2023.102069

PMCID:: PMC9898792

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Select item 1013453015.

POInT_browse: orthology prediction and synteny exploration for paleopolyploid genomes

Mustafa Siddiqui, Gavin C. Conant

BMC Bioinformatics. 2023; 24: 174. Published online 2023 Apr 27. doi: 10.1186/s12859-023-05298-w

PMCID:: PMC10134530

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Select item 1010070916.

Global Increase of Antibiotic Resistance Genes in Conjugative Plasmids

Xiaolong Wang, Hanhui Zhang, Xiang Long, Ximing Xu, Hongqiang Ren, Daqing Mao, Pedro J. J. Alvarez, Yi Luo

Microbiol Spectr. 2023 Mar-Apr; 11(2): e04478-22. Published online 2023 Mar 22. doi: 10.1128/spectrum.04478-22

PMCID:: PMC10100709

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Select item 575336117.

qPrimerDB: a thermodynamics-based gene-specific qPCR primer database for 147 organisms

Kun Lu, Tian Li, Jian He, Wei Chang, Rui Zhang, Miao Liu, Mengna Yu, Yonghai Fan, Jinqi Ma, Wei Sun, Cunmin Qu, Liezhao Liu, Nannan Li, Ying Liang, Rui Wang, Wei Qian, Zhanglin Tang, Xinfu Xu, Bo Lei, Kai Zhang, Jiana Li

Nucleic Acids Res. 2018 Jan 4; 46(Database issue): D1229–D1236. Published online 2017 Aug 21. doi: 10.1093/nar/gkx725

PMCID:: PMC5753361

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Select item 472217418.

OryzaGenome: Genome Diversity Database of Wild Oryza Species

Hajime Ohyanagi, Toshinobu Ebata, Xuehui Huang, Hao Gong, Masahiro Fujita, Takako Mochizuki, Atsushi Toyoda, Asao Fujiyama, Eli Kaminuma, Yasukazu Nakamura, Qi Feng, Zi-Xuan Wang, Bin Han, Nori Kurata

Plant Cell Physiol. 2016 Jan; 57(1): e1. Published online 2015 Nov 16. doi: 10.1093/pcp/pcv171

PMCID:: PMC4722174

Article PDF–562K

Select item 422572519.

PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool

Xinbin Dai, Senjuti Sinharoy, Michael Udvardi, Patrick Xuechun Zhao

BMC Bioinformatics. 2013; 14: 321. Published online 2013 Nov 12. doi: 10.1186/1471-2105-14-321

PMCID:: PMC4225725

Article PDF–601K

Select item 510761020.

Using FlyBase, a Database of Drosophila Genes & Genomes

Steven J. Marygold, Madeline A. Crosby, Joshua L. Goodman, the FlyBase Consortium

Methods Mol Biol. Author manuscript; available in PMC 2017 Jan 1.

Published in final edited form as: Methods Mol Biol. 2016; 1478: 1–31. doi: 10.1007/978-1-4939-6371-3_1

PMCID:: PMC5107610

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PMC Images search for batch-download

Fig. 6

(a) The FlyBase Batch Download interface, using the FlyBase Gene IDs (FBgns) exported from the ACTINS Gene Group as an example. (b) The Batch Download interface for selecting data fields for download (only the top section is shown).

Using FlyBase to Find Functionally Related Drosophila Genes

Methods Mol Biol. ;1757:493-512.
Figure 2

An example output page of PlantTFcat that includes search, sort, and batch download links.

PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool

BMC Bioinformatics. 2013;14:321-321.
Figure 1.

TermLink search example. (A) Search for ‘stem cell’ in TermLink. (B) Select ‘stem cell’ from the FBbt ontology. (C) Click ‘Alleles’ (red dashed circle) to see alleles showing stem-cell-related phenotype. (D) On the resulting hitlist page, select ‘Genes’ (highlighted) from the ‘Convert to’ drop-down menu. (E) Export the list of genes to ‘Batch Download’ (in red and underlined) using the ‘HitList Conversion Tools’ menu. (F) Using the ‘Select fields’ on the batch download page, select the ‘Human Orthologs’ radio button.

FlyBase 102—advanced approaches to interrogating FlyBase

Nucleic Acids Res. 2014 Jan 1;42(Database issue):D780-D788.
Figure 3

The FlyBase ‘Batch Download Reports by ID’ tool. In this example, seven genes are the subject of the query (listed in the ‘Enter List of Ids’ box), the user has selected ‘Document hypertext’ as the output format, and is in the process of selecting which data fields to retrieve.

FlyBase: genes and gene models

Nucleic Acids Res. 2005 Jan 1;33(Database Issue):D390-D395.