Getting Pairwise Sequence alignment From The Muscle Command-Line

Question

[bioinformaticsm28]

The MUSCLE command line doesn't have an option for returning the pairwise sequence alignment. Is there a way to get those alignment(in python)?

for example if I have three sequences Seq1,Seq2 and Seq3:

Tt gives me the aligned sequences as follows:

s1 and s2
s1 and s3
s2 and s3

Answer 1

[Ram]

IMO you'll have to split your sequences into separate input files and run one of these tools for each pair. MUSCLE does not have the option to do combinatorial pairwise alignment.

[bioinformaticsm28]

Thank you.If I sperate may sequencs , may be I lost the value of multiple alignment

[Ram]

Do both MSA and pairwise alignments. And yes, you'll need to switch to Linux/OS X to use most of the tools in Bioinformatics

[bioinformaticsm28]

OK. Thank you.I try to use Emboss, when I use NEEDLE, I get the following errors:

From the window of saved Results

Error: Failed to open filename '-noendweight'
Error: Unable to read sequence '-noendweight'
Died: needle terminated: Bad value for '-bsequence' with -auto defined

and this error from the file stderrfile :

Died: Value required for '-bsequence' before '-gapopen'

[Ram]

Could you maybe give us the exact command you used please?

[bioinformaticsm28]

I do it with the software mEMBOSS

[Ram]

OK, but what was the command? Or is mEMBOSS a GUI application?

[bioinformaticsm28]

It is mEMBOSS a GUI application

[Ram]

The tool should ideally write the actual command it used to either the saved results window or the stderr file. Could you check on that please?

[bioinformaticsm28]

This is what I get

Error: Failed to open filename '-noendweight'
Error: Unable to read sequence '-noendweight'
Died: needle terminated: Bad value for '-bsequence' with -auto defined

[Ram]

That's the error. Does the tool write the command it executes to the log just like it writes the error?

[bioinformaticsm28]

No, it didn't

[Ram]

Ah, that makes debugging a tiny bit harder. Is there a settings or preferences window where you can see the parameters used to run the application?

Answer 2

[Frédéric Mahé]

I think there is a EMBOSS command named "dismat". You could also use python to call the command needle to get pairwise alignments. However, it would be very slow. I suggest to use vsearch:

vsearch --allpairs_global fastafile --acceptall

vsearch offers a variety of output formats. Disclaimer: I am a member of the vsearch team.

[bioinformaticsm28]

Thank you. It works on GNU/Linux or OS X, but not on windows.

[Ram]

Bioinformatics and Windows don't gel well. You might wanna run a Linux VM in your Windows machine or dual boot.

[bioinformaticsm28]

OK.thank you