Question: All vs. all pairwise sequence aligment
0
gravatar for mschmid
2.4 years ago by
mschmid90
Switzerland
mschmid90 wrote:

I have a fasta file with amino acid sequences. Now I want to align every sequence with every other (so it's pairwise). The outcome should be a distance (or similarity, doesn't matter) matrix.

I would like to do local alignment. EDIT: The sequences do NOT have the same length and might just have similar regions partially.

What tool would you suggest?

Ideally I can later do the same with nucleotide sequences.

alignment local fasta • 1.1k views
ADD COMMENTlink modified 2.4 years ago by kloetzl1.0k • written 2.4 years ago by mschmid90
1
gravatar for cool.abbecker
2.4 years ago by
cool.abbecker30 wrote:

Are you really sure you need a pairwise alignment and cannot do a global alignment? It is 1000 times faster and easier.

Use R! https://cran.r-project.org/web/packages/phangorn/phangorn.pdf Page 20

library(ips)
library(phangorn)
setwd("your_working_dir")

x <- read.fas("my_aligned_fasta.fasta")
x <- as.phyDat(x)
y <- dist.ml(x, whatever you need)
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by cool.abbecker30

This solution expects all seqs to be the same length, right?

ADD REPLYlink written 2.4 years ago by mschmid90

Yes. To compare distances they must be aligned.

ADD REPLYlink written 2.4 years ago by cool.abbecker30
0
gravatar for fhsantanna
2.4 years ago by
fhsantanna440
Brazil
fhsantanna440 wrote:

ClustalO can output a distance matrix (--distmat-out=<file> option).

ADD COMMENTlink written 2.4 years ago by fhsantanna440

ClustalO does multiple sequence alignment, not pairwise, right?

ADD REPLYlink written 2.4 years ago by mschmid90
0
gravatar for buchfink
2.4 years ago by
buchfink140
buchfink140 wrote:

You can try the DIAMOND aligner: https://github.com/bbuchfink/diamond

ADD COMMENTlink written 2.4 years ago by buchfink140
0
gravatar for kloetzl
2.4 years ago by
kloetzl1.0k
European Union
kloetzl1.0k wrote:

If all you want is a distance matrix, why bother aligning at all? Try http://spaced.gobics.de/ for amino acids.

ADD COMMENTlink written 2.4 years ago by kloetzl1.0k
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