Example Workflows

The following sample workflows are included in PipeWorks. Once conceptualized, many workflows can be assembled in under 10 minutes using the drag-and-drop interface.

Please click on the images for full-sized screen shots.

Connect Sequential Searches for More Powerful Annotation

In this workflow, adding a filter step enables you to route results data based upon percent identity, e-value, bitscore, gap percentage or score count. At each search step, you can view multiple results to help optimize your workflows.

1. Input sequences are processed with Tera-BLAST
2. Sequences that generate no hits—or score below your filter threshold—are compared to Swiss-Prot using Smith-Waterman (S-W).
3. Sequences that are not confidently identified by BLAST or S-W are routed to an HMM search that attempts to link them to particular superfamilies or protein families
   

Automate and Schedule Repetitive Tasks

• PipeWorks’ Database Updater workflow downloads database sources from one or more FTP sites, then formats them for local searching.
• Workflows can also employ the File Grabber to retrieve a remote set of query sequences.
• All workflows can be scheduled by date or frequency.

Merge Results, Embed Perl Scripts

You can also merge multiple sets of extracted sequences to serve as the input for additional operations. You can also embed custom Perl and Python scripts into workflows.

Search, Filter and Analyze

1. Use Tera-BLASTP to compare new protein sequences to a custom protein database
2. Filter the results by e-value
3. High-confidence hits are processed by the EMBOSS tool Pepinfo (a). Pepinfo’s hydrophobicity plots and residue histograms will be displayed for each hit.
4. Results that score below the filter threshold (b) are routed to a more sensitive Smith-Waterman search

Build Hidden Markov Models to Expand Protein Families

1. Generate a multiple sequence alignment from a protein family using ClustalW
2. Build a hidden Markov model (HMM) for searching UniProt

The unique combination of PipeWorks and CodeQuest enables you to process high-throughput EST and protein annotation workflows, as well as HMM-heavy metagenomics projects. Your entire lab can design and process workflows on a resource-friendly desktop system to advance their genomics projects or drug discovery efforts.