clustal_omega.md 5.9 KB
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1.  [HCC-DOCS](index.html)
2.  [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
3.  [HCC Documentation](HCC-Documentation_332651.html)
4.  [Running Applications](Running-Applications_7471153.html)
5.  [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
6.  [Alignment Tools](Alignment-Tools_8193288.html)

<span id="title-text"> HCC-DOCS : Clustal Omega </span>
=======================================================

Created by <span class="author"> Adam Caprez</span>, last modified by
<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016

| Name          | Version | Resource |
|---------------|---------|----------|
| clustal-omega | 1.2     | Tusker   |

|               |     |       |
|---------------|-----|-------|
| clustal-omega | 1.2 | Crane |

 

Clustal Omega
(<a href="http://www.clustal.org/omega/" class="external-link">http://www.clustal.org/omega/</a>)
is a general purpose multiple sequence alignment (MSA) tool used mainly
with protein, as well as DNA and RNA sequences. Clustal Omega is fast
and scalable aligner that can align datasets of hundreds of thousands of
sequences in reasonable time.

The general usage of Clustal Omega is:

**General Clustal Omega Usage**

``` syntaxhighlighter-pre
clustalo -i input_file.fasta -o output_file.fasta [options]
```

where **input\_file.fasta** is the multiple sequence input file in
*fasta* format, and **output\_file.fasta** is the multiple sequence
alignment output file in *fasta* format.  
Clustal Omega accepts 3 types of sequence input files:

-   sequence file with aligned/unaligned sequences

<!-- -->

-   multiple alignment in a file/profile of aligned sequences

<!-- -->

-   Hidden Markov Model (HMM) 

These input files must contain at least 2 sequences and must be in one
of the following MSA file formats: **a2m****fa\[sta\]**,
**clu\[stal\]**, **msf**, **phy\[lip\]**, **selex**, **st\[ockholm\]**,
**vie\[nna\]**. Moreover, if not specified, the generated output file is
in *fasta* format.

More Clustal Omega options can be found by typing:

**Additional Clustal Omega Options**

``` syntaxhighlighter-pre
[<username>@login.tusker~]$ clustalo -h
```

  
Running Clustal Omega on Tusker with input
file **input\_reads.fasta** with **8 threads** and **10GB memory** is
shown below:

**clustal\_omega.submit**

\#!/bin/sh  
\#SBATCH --job-name=Clustal\_Omega  
\#SBATCH --nodes=1  
\#SBATCH --ntasks-per-node=8  
\#SBATCH --time=10:00:00  
\#SBATCH --mem=10gb  
\#SBATCH --output=ClustalOmega.%J.out  
\#SBATCH --error=ClustalOmega.%J.err

 

|                               |
|-------------------------------|
| module load clustal-omega/1.2 |

clustalo -i input\_reads.fasta -o output\_msa.sto --outfmt=st
--threads=$SLURM\_NTASKS\_PER\_NODE

The output file **output\_msa.sto** contains the resulting multiple
sequence alignments in Stockholm format (**--outfmt=st**).

Moreover, if you change the command above with:

**Clustal Omega with De-align Option**

``` syntaxhighlighter-pre
clustalo -i input_reads.sto --dealign -v
```

Clustal Omega will read the input file in Stockholm format, de-align the
sequences, and then re-align them, printing progress report in meanwhile
(**-v**). Because it is not specified, the output will be in the default
**fasta** format.

 

**Clustal Omega Output**

The basic Clustal Omega output produces one alignment file in the
specified output format. More intermediate outputs can be generated
using specific Clustal Omega options, such
as: **--distmat-out=&lt;file&gt;** (*pairwise distance matrix output
file*) and **--guidetree-out=&lt;file&gt;** (*guide tree output file*).

**  
Useful Information**

In order to test the Clustal Omega performance on Tusker, we used three
DNA and protein input fasta files: **data\_1. fasta, data\_2. fasta,
data\_3.fasta**. Some statistics about the input files and the time and
memory resources required for Clustal Omega are shown on the table
below:

<table style="width:100%;">
<colgroup>
<col style="width: 14%" />
<col style="width: 14%" />
<col style="width: 14%" />
<col style="width: 14%" />
<col style="width: 14%" />
<col style="width: 14%" />
<col style="width: 14%" />
</colgroup>
<thead>
<tr class="header">
<th> </th>
<th><p><strong>total # of sequences</strong></p></th>
<th><p><strong>average sequence length</strong></p></th>
<th><p><strong>total size in MB</strong></p></th>
<th><p><strong>Clustal Omega required time</strong></p></th>
<th><p><strong>Clustal Omega required memory</strong></p></th>
<th># of used CPUs</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td><p><strong>data_1.fasta</strong></p></td>
<td><p>1,200</p></td>
<td><p>510.17</p></td>
<td><p>641 KB</p></td>
<td><p>~ 5 minutes</p></td>
<td><span>~ 65 MB</span></td>
<td>8</td>
</tr>
<tr class="even">
<td><p><strong>data_2.fasta</strong></p></td>
<td><p>5,715</p></td>
<td><p>174.20</p></td>
<td><p>1,100 KB</p></td>
<td>~ 5 minutes</td>
<td><p>~ 140 MB</p></td>
<td><p>8</p></td>
</tr>
<tr class="odd">
<td><p><strong>data_3.fasta</strong></p></td>
<td><p>93,675</p></td>
<td><p>94.29</p></td>
<td><p>11,000 KB</p></td>
<td><p>~ 30 minutes</p></td>
<td><p>~ 2 GB</p></td>
<td><p>8</p></td>
</tr>
</tbody>
</table>

Attachments:
------------

<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[crane\_clustal\_omega\_version.xsl](attachments/9470379/9863812.xsl)
(application/octet-stream)  
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[cb\_clustal\_omega\_module.xsl](attachments/9470379/9863813.xsl)
(application/octet-stream)  
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[tusker\_clustal\_omega\_version.xsl](attachments/9470379/9863814.xsl)
(application/octet-stream)  
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[crane\_modules.xml](attachments/9470379/9863815.xml)
(application/octet-stream)  
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[tusker\_modules.xml](attachments/9470379/9863816.xml)
(application/octet-stream)