I'm writing a script where I would like to implement alignments to a reference sequence (so NOT just multiple sequence alignment via e.g. clustal's REST web service).
I know applications that can do this, but then it's from a GUI. I also know plenty of command line way to do multiple sequence alignments, but not aligning to a reference sequence. But I just can't believe it doesn't exist?
Clustalw, tcoffe and muscle include options to align a reference sequence to a profile (aln). Here goes the command line for clustalw;
clustalw -profile1=your.aln -profile2=refseq.fasta -sequences
Hi,
you can use MUSCLE. It allows you to align two alignments with each other (known as profile-profile alignment),
For single sequence in the profile:-
muscle -profile -in1 first.fasta -in2 second..fasta -out combined_result.fasta
this aligns the alignments in the two files first.fasta and second.fasta to each other and writes them to combined_result.fasta
You can also do the same profiles thing with Mafft.
http://mafft.cbrc.jp/alignment/software/addsequences.html
https://mafft.cbrc.jp/alignment/software/
with ClustalW2:-
clustalw2 -profile1=data.fa -sequences -profile2=first.fa
assuming one seq is first.fa and the prealigned others are in data.fa
you can also look AVID
Bray, N., Dubchak, I. and Pachter, L. (2003) AVID: A Global Alignment Program. Genome Res., 13:97
Hi both Pedro A Reche and Dilraj Kaur , thanks for the suggestions. Just to be sure I understand, you say I would need to pre-align my sequences, and then align the (pre-)alignment to my reference sequence?
The 10s - 100s of sequences I have, that need to align to each "reference" are short, and won't necessarily align to the same part of the reference. If they are pre-aligned, wouldn't they be forced to align to the same part? Taking the info from the pre-alignment (that I don't want)? Or am I misunderstanding what they do? I'm looking more for something like the "align to reference" function of many sequence viewer/manipulator GUI software (like e.g. CLC or Geneious). Just usable from command line.
I did look at Avid before posting here, but the link in the paper is dead, and I couldn't find it elsewhere (researchers, don't host software on your own servers, have a central university repo for that! One that persists after the researcher is gone!). If you have a link to where it is now, I'd appreciate it.
You can do both, align two profiles (alinments) or align sequence/s to a profile. In the first case you will need two prealigned set of sequences (profiles) and in the second only one.
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