Question: Getting Pairwise Sequence alignment From The Muscle Command-Line
0
gravatar for bioinformaticsm28
4.6 years ago by
bioinformaticsm280 wrote:

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:

it gives me the aligned sequences as follows:

s1 and s2

s1 and s3

s2 and s3
alignment sequence python • 2.8k views
ADD COMMENTlink modified 4.6 years ago by Frédéric Mahé2.9k • written 4.6 years ago by bioinformaticsm280
0
gravatar for RamRS
4.6 years ago by
RamRS23k
Houston, TX
RamRS23k wrote:

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.

ADD COMMENTlink written 4.6 years ago by RamRS23k

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

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by bioinformaticsm280

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

ADD REPLYlink written 4.6 years ago by RamRS23k

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'
ADD REPLYlink written 4.6 years ago by bioinformaticsm280

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

ADD REPLYlink written 4.6 years ago by RamRS23k

I do it with the software mEMBOSS

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by bioinformaticsm280

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

ADD REPLYlink written 4.6 years ago by RamRS23k

it is mEMBOSS a GUI application

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by bioinformaticsm280

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?

ADD REPLYlink written 4.6 years ago by RamRS23k

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
ADD REPLYlink written 4.6 years ago by bioinformaticsm280

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

ADD REPLYlink written 4.6 years ago by RamRS23k

no, it didn't

ADD REPLYlink written 4.6 years ago by bioinformaticsm280

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?

ADD REPLYlink written 4.6 years ago by RamRS23k
0
gravatar for Frédéric Mahé
4.6 years ago by
France, Montpellier, CIRAD
Frédéric Mahé2.9k wrote:

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.

ADD COMMENTlink written 4.6 years ago by Frédéric Mahé2.9k

thank you. but, it works on GNU/Linux or OS X. but not  on windows

ADD REPLYlink written 4.6 years ago by bioinformaticsm280

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

ADD REPLYlink written 4.6 years ago by RamRS23k

OK.thank you

ADD REPLYlink written 4.6 years ago by bioinformaticsm280
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