Sequence analysis tools, programmatically

 

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Providing access to core analytical tools and protein and nucleotide sequence databases is central to the EMBL-EBI’s mission. Tools such as InterProScan, BLAST+, PSI-SEARCH, Clustal Omega and HMMER3 are but a few of more than 60 sequence analysis tools accessible using SOAP and RESTful API Web Services. There are client applications written in a variety of languages including Python, Perl and Java for many of these tools which can be integrated directly into your bioinformatics pipelines.

This webinar took place on 18th July 2017. It introduces these client applications and demonstrates how they can be used to form simple but effective workflows. It focuses on clients that demonstrate the RESTful API to tools such as blast+ and Clustal Omega, and data retrieval tools such as dbfetch.

This webinar is for anyone familiar with running bioinformatics tools from the command-line (Linux terminal, Windows CMD or PowerShell).

The webinar includes:

  • An introduction to EMBL-EBI tools RESTful clients (0:50)
  • Where to get the clients (2:52)
  • How to run the clients (5:43)
  • How to run a simple pipeline manually using a shell script and CWL (14:05)
  • Where to get help and support (20:31)

You can download the slides and example scripts using these links.

You can explore all of the EMBL-EBI's tools, resources and databases on our services page.

On the services page will also find a list of tools and resources that can be accessed programmatically with links to the relevant help pages and documentation.

Get in touch with us if you need help with any of the tools and resources.