SequenceServer VICE application in DE¶
Uses SequenceServer 2.0
The tutorial guides you how to use SequenceServer VICE app in discovery enviornment. Custom Blast databases can be created using Create BLAST database app.
About SequenceServer¶
Sequenceserver is a modern graphical interface for BLAST designed to increase the productivity of biologist researchers performing and interpreting BLAST searches (Priyam et al., 2015).
- Smart user interface automagically figures out the appropriate BLAST method for the given query and selected databases.
- Detects sequence type of FASTA files and prompts to turn them into BLAST databases.
- Graphical overview of results naturally separates strong from weak hits (by evalue).
- GenBank style visualisation of hit sequences - residues grouped in multiples of five.
- Download hit sequences in FASTA format, and alignment data in tab-delimited and XML format for further analysis.
Launch SequenceServer with the default database¶
- Login to the Discovery Environment.
- CLick on “Apps” tab in the Discovery Enviornment and search for “SequenceServer”.
- Click on the app icon.
- Change the name of the analysis and output folder as needed or leave for defaults.
- Under “Input” leave the default database or browse through the datastore and change the path to a custom database. Change the number of CPUs as per requirement.
- Under “Resource Requirements” request resources as needed or leave for defaults
- Click Launch Analysis. You will receive a notification that the job has been submitted and running. Click on ‘Access your analysis here’ link.
- Once the analysis is launched, you will see the SequenceServer user interface. Input your query sequences and click Blast.
Prerequisites¶
Downloads, access, and services¶
In order to complete this tutorial you will need access to the following services/software
| Prerequisite | Preparation/Notes | Link/Download |
|---|---|---|
| CyVerse account | You will need a CyVerse account to complete this exercise | CyVerse User Portal |
Platform(s)¶
We will use the following CyVerse platform(s):
| Platform | Interface | Link | Platform Documentation | Quick Start |
|---|---|---|---|---|
| Data Store | GUI/Command line | Data Store | Data Store Manual | Data Store Guide |
| Discovery Environment | Web/Point-and-click | Discovery Environment | DE Manual | Discovery Environment Guide |
Application(s) used¶
Discovery Environment App(s):
| App name | Version | Description | App link | Notes/other links |
|---|---|---|---|---|
| Create BLAST database | 2.6.0 | Make BLAST database | DE Application URL | Original App Documentation |
Input and example data¶
In order to complete this tutorial you will need to have the following inputs prepared
| Input File(s) | Format | Preparation/Notes | Example Data |
|---|---|---|---|
| BLAST Database | BLAST Database | A default database is already provided with the app. Browse through the data store to use any custom database for the app. | Reference viroids nucleotide database (iplantcollaborative > example_data > sequenceserver > db) |
References
Priyam A, Woodcroft BJ, Rai V, Munagala A, Moghul I, Ter F, Gibbins MA, Moon H, Leonard G, Rumpf W & Wurm Y. 2015. Sequenceserver: a modern graphical user interface for custom BLAST databases. biorxiv doi: 10.1101/033142.
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