MSA-PAD Genome Mode Multiple DNA Sequence Alignment Framework - Input Submission and email notification

BioVeL – Biodiversity Virtual e-Laboratory

Workflow Documentation

Name:Perform a Multiple DNA sequence alignment coding for multiple/single protein domains

Capacities Programme of Framework 7: EC e-Infrastructure Programme – e-Science Environments - INFRA-2011-1.2.1 Grant Agreement No: 283359 Project Co-ordinator: Mr Alex Hardisty Project Homepage: [http://www.biovel.eu][1]

[1]: http://www.biovel.eu

## 1 Description

This workflow is used to submit the multiple alignment job. Once the computation is finished the user will receive an email notification indicating the obtained output address. The workflow at work translates DNA sequences following a user defined genetic code and one or more open reading frame/s. It devides the translated sequence at each stop codon into separate sequences. It searches, using hmmsearch (HMMer3.0 package), translated amino acid sequences against a mirror of PFAM-A conserved domains database. It performs a MSA of either single or multiple protein domains coding sequences. The workflow finally merges the sequence fragments coding for unique PFAM domains.

## 2 General

**2.1 Name of the workflow and myExperiment +BiodiversityCatalogue identifiers** Name: Perform a Multiple DNA sequence alignment coding for multiple/single protein domains Download info: [http://www.myexperiment.org/packs/371.html][2] BiodiversityCatalogue entry:

**2.2 Date, version and licensing** Last [updated:30/07/14][3] @ 16:00:00 Version: 4 Licensing: Creative Commons Attribution ShareAlike CC-BY- SA

**2.3 How to cite this workflow**

These results come from the processing of public data data (public repositories) through BioVeL's services ([www.biovel.eu][4]). BioVeL is funded by the EU’s Seventh Framework Program, grant no. 283359. Use the article [http://journal.embnet.org/index.php/embnetjournal/article/view/557][6]

[3]: http://www.myexperiment.org/packs/371.html [4]: http://updated:21/02/13 [5]: http://www.biovel.eu [6]: http://journal.embnet.org/index.php/embnetjournal/article/view/557

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3. Scientific Specifications

**3.1. Keywords:** MSA, coding sequences, back-translation, merger, MrBayes. **3.2. Scientific workflow description:**

Arguments: 1- DNA sequences coding for single or multiple protein domain in fasta format 2- One of the following genetic codes: 1,6,10,12,15,2,3,4,5,9,13,14,16,21,22,23,11,25 3- Reading frame(s) The different step for a complete phylogenetic inference are in this pack divided as following:

The email address and a filename should be provided to receive the notification of computation completion, therefore the availabilty of the results to be downloaded.

## 4. Technical Specifications

**4.1. Execution environment and installation requirements**

The workflows is tested in Taverna Workbench Biodiversity 2.5.0.

[Taverna workbench installation][7] [7]: http://www.taverna.org.uk/download/workbench/2-5/biodiversity/

## 5. Support For questions with using the workflow, please write [support@biovel.eu][8]. For definitions of technical and biological terms, please visit the BioVeL glossary page: [https://wiki.biovel.eu/display/BioVeL/Glossary][9]

[8]: mailto:support@biovel.eu [9]: https://wiki.biovel.eu/display/BioVeL/Glossary

## 7. Bibliography

1. Donvito, G., et al. (2012) The BioVeL Project: Robust phylogenetic workflows running on the GRID. Proceedings of the EGI Community Forum 2012/EMI Second Technical Conference (EGICF12-EMITC2). 26-30 March, 2012. Munich, Germany. Published online at http://pos.sissa.it/cgi-bin/reader/conf.cgi?confid=162, id. 29. pp. 29.
2. Eddy, S.R. (2011) Accelerated Profile HMM Searches, PLoS computational biology, 7, e1002195.