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Sequenceserver: a modern graphical user interface for custom BLAST databases

Anurag Priyam, Ben J. Woodcroft, Vivek Rai, Alekhya Munagala, Ismail Moghul, Filip Ter, Mark Anthony Gibbins, HongKee Moon, Guy Leonard, Wolfgang Rumpf, View ORCID ProfileYannick Wurm
doi: https://doi.org/10.1101/033142
Anurag Priyam
1School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom.
2Department of Mechanical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India.
115Bases Limited, London E9 7DR, United Kingdom.
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Ben J. Woodcroft
3Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Queensland, Australia.
115Bases Limited, London E9 7DR, United Kingdom.
12Previous address: Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Victoria, Australia.
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Vivek Rai
4Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India.
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Alekhya Munagala
5Department of Mathematics, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India.
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Ismail Moghul
1School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom.
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Filip Ter
6School of Electronic Engineering and Computer Science, Queen Mary University of London, London E1 4NS, United Kingdom.
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Mark Anthony Gibbins
7Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, United Kingdom.
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HongKee Moon
8Scientific Computing Facility, Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr 108, 01307 Dresden, Germany.
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Guy Leonard
9Biosciences, University of Exeter, Geoffrey Pope Building, Exeter EX4 4QD, United Kingdom.
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Wolfgang Rumpf
10The Graduate School, University of Maryland, University College, Largo, MD, 20774, United States; and The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, 43205, United States
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Yannick Wurm
1School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom.
115Bases Limited, London E9 7DR, United Kingdom.
13Previous address: Department of Ecology and Evolution and Swiss Institue of Bioinformatics, Université de Lausanne, 1015 Lausanne, Switzerland.
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  • ORCID record for Yannick Wurm
  • For correspondence: y.wurm@qmul.ac.uk
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Abstract

The dramatic drop in DNA sequencing costs has created many opportunities for novel biological research. These opportunities largely rest upon the ability to effectively compare newly obtained and previously known sequences. This is commonly done with BLAST, yet using BLAST directly on new datasets requires substantial technical skills or helpful colleagues. Furthermore, graphical interfaces for BLAST are challenging to install and largely mimic underlying computational processes rather than work patterns of researchers.

We combined a user-centric design philosophy with sustainable software development approaches to create Sequenceserver (http://sequenceserver.com), a modern graphical user interface for BLAST. Sequenceserver substantially increases the efficiency of researchers working with sequence data. This is due to innovations at three levels. First, our software can be installed and used on custom datasets extremely rapidly for personal and shared applications. Second, based on analysis of user input and simple algorithms, Sequenceserver reduces the amount of decisions the user must make, provides interactive visual feedback, and prevents common potential errors that would otherwise cause erroneous results. Finally, Sequenceserver provides multiple highly visual and text-based output options that mirror the requirements and work patterns of researchers. Together, these features greatly facilitate BLAST analysis and interpretation and thus substantially enhance researcher productivity.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted November 27, 2015.
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Sequenceserver: a modern graphical user interface for custom BLAST databases
Anurag Priyam, Ben J. Woodcroft, Vivek Rai, Alekhya Munagala, Ismail Moghul, Filip Ter, Mark Anthony Gibbins, HongKee Moon, Guy Leonard, Wolfgang Rumpf, Yannick Wurm
bioRxiv 033142; doi: https://doi.org/10.1101/033142
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Sequenceserver: a modern graphical user interface for custom BLAST databases
Anurag Priyam, Ben J. Woodcroft, Vivek Rai, Alekhya Munagala, Ismail Moghul, Filip Ter, Mark Anthony Gibbins, HongKee Moon, Guy Leonard, Wolfgang Rumpf, Yannick Wurm
bioRxiv 033142; doi: https://doi.org/10.1101/033142

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