Question: Aligning One Protein Sequence With A Multiple Sequence Alignment
gravatar for Reyhaneh
8.7 years ago by
United Kingdom
Reyhaneh480 wrote:

Given one protein sequence and a multiple sequence alignment(MSA) of a set of proteins, I want to align the protein sequence with that MSA with out changing the MSA. Do you know any tool that is cable of doing this?

Thanks in advance.

sequence alignment multiple msa • 7.2k views
ADD COMMENTlink modified 3.6 years ago by kamr1002000 • written 8.7 years ago by Reyhaneh480
gravatar for Andreas
8.7 years ago by
Andreas2.5k wrote:

Paulo is right: Clustal could always do this. Clustal2 and Clustal-Omega have something called profile alignment-mode, which allows you to align two pre-aligned sequence-sets (profiles) in one step. Your one sequence can also be seen as a profile. Clustal2 furthermore had a special mode, which allows you to align (unaligned) sequences one by one to a profile (see -sequences flag below). This is interesting if you have many unaligned sequences that you want to align to a profile.

Assuming your one sequence is called one.fa and the prealigned others are in prof1.fa then the command-line would look like this:


clustalw2  -profile1=prof1.fa -sequences -profile2=one.fa

The -sequences flag would align every (unaligned) sequence in profile2 to profile1. In your case you have just one sequence, so the flag doesn't do much and you could also leave it away.

Clustal Omega only knows about profile-profile alignment, so there's no -sequence flag. But again, in your case a normal profile-profile alignment will do, as the one sequence will be treated as an alignment.

clustalo  --profile1 prof1.fa --profile2 one.fa


ADD COMMENTlink modified 8.7 years ago • written 8.7 years ago by Andreas2.5k

Thank you so much for this complete answer. It is exactly what I wanted.

ADD REPLYlink written 8.7 years ago by Reyhaneh480
gravatar for Paulo Nuin
8.7 years ago by
Paulo Nuin3.7k
Paulo Nuin3.7k wrote:

Best bet is to use ClustalW and use your original MSA as a profile where the other sequence will be aligned to. Check the program's documentation on how to do profile alignment.

ADD COMMENTlink written 8.7 years ago by Paulo Nuin3.7k
gravatar for aidan-budd
8.1 years ago by
aidan-budd1.9k wrote:

You can (or at least could - I haven't done it in a while) do this with MUSCLE

MUSCLE allows you to align two alignments with each other (known as profile-profile alignment), although this functionality is also only available from the command line, not e.g. via the EBI MUSCLE web server. If one of the profiles contains just a single sequence, then you can do what you've asked about in the question

muscle -profile -in1 aln1.fasta -in2 aln2.fasta -out combinedAlignment.fasta

this aligns the alignments in the two files aln1.fasta and aln2.fasta to each other and writes them to combinedAlignment.fasta

ADD COMMENTlink written 8.1 years ago by aidan-budd1.9k
gravatar for Biojl
8.1 years ago by
Biojl1.7k wrote:

You can also do the same profiles thing with Mafft, It's one of the best (and fastests) aligners available:

ADD COMMENTlink written 8.1 years ago by Biojl1.7k
gravatar for Suzanne
4.8 years ago by
Dundee, Scotland
Suzanne70 wrote:

Clustal Omega, Clustal W, Mafft, Muscle, Tcoffee and Probcons multiple sequence alignment tools all work in Jalview via the Jalview web service. See their Jalview YouTube Training Channel.

ADD COMMENTlink written 4.8 years ago by Suzanne70
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