Sequenceserver: a modern graphical user interface for custom BLAST databases.

Anurag Priyam; Ben J Woodcroft; Vivek Rai; Ismail Moghul; Alekhya Mungala; Filip Ter; Hiten Chowdhary; Iwo Lukasz Pieniak; Mark Anthony Gibbins; HongKee Moon; Austin Davis-Richardson; Mahmut Uludag; Nathan S Watson-Haigh; Richard Challis; Hiroyuki Nakamura; Emeline Favreau; Esteban Gόmez Cifuentes; Tomás Pluskal; Guy Leonard; Wolfgang Rumpf; Yannick Wurm

doi:10.1093/molbev/msz185

Sequenceserver: a modern graphical user interface for custom BLAST databases.

Anurag Priyam, Ben J Woodcroft, Vivek Rai, Ismail Moghul, Alekhya Mungala, Filip Ter, Hiten Chowdhary, Iwo Lukasz Pieniak, Mark Anthony Gibbins, HongKee Moon, Austin Davis-Richardson, Mahmut Uludag, Nathan S Watson-Haigh, Richard Challis, Hiroyuki Nakamura, Emeline Favreau, Esteban Gόmez Cifuentes, Tomás Pluskal, Guy Leonard, Wolfgang RumpfYannick Wurm

Computer, Electrical and Mathematical Sciences and Engineering

Research output: Contribution to journal › Article › peer-review

144 Scopus citations

Abstract

Comparing newly obtained and previously known nucleotide and amino-acid sequences underpins modern biological research. BLAST is a well-established tool for such comparisons but is challenging to use on new datasets. We combined a user-centric design philosophy with sustainable software development approaches to create Sequenceserver, a tool for running BLAST and visually inspecting BLAST results for biological interpretation. Sequenceserver uses simple algorithms to prevent potential analysis errors, and provides flexible text-based and visual outputs to support researcher productivity. Our software can be rapidly installed for use by individuals or on shared servers. Sequenceserver is AGPLv3-licensed at https://sequenceserver.com.

Original language	English (US)
Pages (from-to)	2922-2924
Number of pages	3
Journal	Molecular biology and evolution
Volume	36
Issue number	12
DOIs	https://doi.org/10.1093/molbev/msz185
State	Published - Aug 14 2019

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: We thank the many Sequenceserver users and contributors for their input. During the creation of Sequenceserver YW was funded by an ERC grant to Laurent Keller. BJW was supported by the United States Department of Energy (DE-SC0004632). While writing this manuscript, YW and AP were supported by BBSRC (BB/K004204/1) and NERC (NE/L00626X/1).

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10.1093/molbev/msz185

https://repository.kaust.edu.sa/bitstream/10754/656486/1/msz185.pdf

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Priyam, A., Woodcroft, B. J., Rai, V., Moghul, I., Mungala, A., Ter, F., Chowdhary, H., Pieniak, I. L., Gibbins, M. A., Moon, H., Davis-Richardson, A., Uludag, M., Watson-Haigh, N. S., Challis, R., Nakamura, H., Favreau, E., Cifuentes, E. G., Pluskal, T., Leonard, G., ... Wurm, Y. (2019). Sequenceserver: a modern graphical user interface for custom BLAST databases. Molecular biology and evolution, 36(12), 2922-2924. https://doi.org/10.1093/molbev/msz185

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title = "Sequenceserver: a modern graphical user interface for custom BLAST databases.",

abstract = "Comparing newly obtained and previously known nucleotide and amino-acid sequences underpins modern biological research. BLAST is a well-established tool for such comparisons but is challenging to use on new datasets. We combined a user-centric design philosophy with sustainable software development approaches to create Sequenceserver, a tool for running BLAST and visually inspecting BLAST results for biological interpretation. Sequenceserver uses simple algorithms to prevent potential analysis errors, and provides flexible text-based and visual outputs to support researcher productivity. Our software can be rapidly installed for use by individuals or on shared servers. Sequenceserver is AGPLv3-licensed at https://sequenceserver.com.",

author = "Anurag Priyam and Woodcroft, {Ben J} and Vivek Rai and Ismail Moghul and Alekhya Mungala and Filip Ter and Hiten Chowdhary and Pieniak, {Iwo Lukasz} and Gibbins, {Mark Anthony} and HongKee Moon and Austin Davis-Richardson and Mahmut Uludag and Watson-Haigh, {Nathan S} and Richard Challis and Hiroyuki Nakamura and Emeline Favreau and Cifuentes, {Esteban Gόmez} and Tom{\'a}s Pluskal and Guy Leonard and Wolfgang Rumpf and Yannick Wurm",

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: We thank the many Sequenceserver users and contributors for their input. During the creation of Sequenceserver YW was funded by an ERC grant to Laurent Keller. BJW was supported by the United States Department of Energy (DE-SC0004632). While writing this manuscript, YW and AP were supported by BBSRC (BB/K004204/1) and NERC (NE/L00626X/1).",

year = "2019",

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doi = "10.1093/molbev/msz185",

language = "English (US)",

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Priyam, A, Woodcroft, BJ, Rai, V, Moghul, I, Mungala, A, Ter, F, Chowdhary, H, Pieniak, IL, Gibbins, MA, Moon, H, Davis-Richardson, A, Uludag, M, Watson-Haigh, NS, Challis, R, Nakamura, H, Favreau, E, Cifuentes, EG, Pluskal, T, Leonard, G, Rumpf, W & Wurm, Y 2019, 'Sequenceserver: a modern graphical user interface for custom BLAST databases.', Molecular biology and evolution, vol. 36, no. 12, pp. 2922-2924. https://doi.org/10.1093/molbev/msz185

TY - JOUR

T1 - Sequenceserver: a modern graphical user interface for custom BLAST databases.

AU - Priyam, Anurag

AU - Woodcroft, Ben J

AU - Rai, Vivek

AU - Moghul, Ismail

AU - Mungala, Alekhya

AU - Ter, Filip

AU - Chowdhary, Hiten

AU - Pieniak, Iwo Lukasz

AU - Gibbins, Mark Anthony

AU - Moon, HongKee

AU - Davis-Richardson, Austin

AU - Uludag, Mahmut

AU - Watson-Haigh, Nathan S

AU - Challis, Richard

AU - Nakamura, Hiroyuki

AU - Favreau, Emeline

AU - Cifuentes, Esteban Gόmez

AU - Pluskal, Tomás

AU - Leonard, Guy

AU - Rumpf, Wolfgang

AU - Wurm, Yannick

N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: We thank the many Sequenceserver users and contributors for their input. During the creation of Sequenceserver YW was funded by an ERC grant to Laurent Keller. BJW was supported by the United States Department of Energy (DE-SC0004632). While writing this manuscript, YW and AP were supported by BBSRC (BB/K004204/1) and NERC (NE/L00626X/1).

PY - 2019/8/14

Y1 - 2019/8/14

N2 - Comparing newly obtained and previously known nucleotide and amino-acid sequences underpins modern biological research. BLAST is a well-established tool for such comparisons but is challenging to use on new datasets. We combined a user-centric design philosophy with sustainable software development approaches to create Sequenceserver, a tool for running BLAST and visually inspecting BLAST results for biological interpretation. Sequenceserver uses simple algorithms to prevent potential analysis errors, and provides flexible text-based and visual outputs to support researcher productivity. Our software can be rapidly installed for use by individuals or on shared servers. Sequenceserver is AGPLv3-licensed at https://sequenceserver.com.

AB - Comparing newly obtained and previously known nucleotide and amino-acid sequences underpins modern biological research. BLAST is a well-established tool for such comparisons but is challenging to use on new datasets. We combined a user-centric design philosophy with sustainable software development approaches to create Sequenceserver, a tool for running BLAST and visually inspecting BLAST results for biological interpretation. Sequenceserver uses simple algorithms to prevent potential analysis errors, and provides flexible text-based and visual outputs to support researcher productivity. Our software can be rapidly installed for use by individuals or on shared servers. Sequenceserver is AGPLv3-licensed at https://sequenceserver.com.

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U2 - 10.1093/molbev/msz185

DO - 10.1093/molbev/msz185

M3 - Article

C2 - 31411700

SN - 0737-4038

VL - 36

SP - 2922

EP - 2924

JO - Molecular biology and evolution

JF - Molecular biology and evolution

IS - 12

ER -

Sequenceserver: a modern graphical user interface for custom BLAST databases.

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