How many sequences can it align?

The aligner is a graph-based partial-order alignment, so it accepts an arbitrary number of sequences rather than a fixed pair. Practical limits come from the machine, since the work happens in the browser.

Are my sequences uploaded anywhere?

No. The alignment runs client-side in the browser and the sequences are held in the page, so nothing is sent to a server.

Sequencing

Multiple Sequence Alignment

Align a set of sequences and read the result as an alignment you can navigate: per-sequence identity, column conservation, and the scores that quantify the alignment. The aligner runs locally, so a set of unpublished sequences stays on the machine.

Open Multiple Sequence Alignment Open the Alignment sample sample

Three real families — 8 cricket COI genes, 19 divergent HIV-1 env genes and three globins — so mode, matrix and gap cost change the answer, plus the real Pfam kinase profile to screen against

What it does

01Partial-order alignment (POA), which represents the alignment as a graph rather than a fixed profile
02Adjustable alignment mode and scoring parameters
03Per-sequence identity, sortable, so the outlier in a set is immediate
04Alignment scores computed over the finished alignment
05Aligned FASTA and CLUSTAL export
06Sequences taken from the open project, pasted in, or imported from a file

What it runs on

The aligner is a port of poapy (partial-order alignment, GPL-3), golden-tested byte for byte against the poapy command line, with alignment scores ported from pyMSA. The panel runs on @ports/ace, @ports/apr, @ports/chromatogram, @ports/hmm, @ports/msa, @ports/msa-alphabet, @ports/msa-options, @ports/phylo, @ports/primer, @ports/rnafold.

Everything runs client-side. Files are parsed in the browser and projects are saved on this machine, so an unpublished sequence is never uploaded.

Questions

How many sequences can it align?: The aligner is a graph-based partial-order alignment, so it accepts an arbitrary number of sequences rather than a fixed pair. Practical limits come from the machine, since the work happens in the browser.
Are my sequences uploaded anywhere?: No. The alignment runs client-side in the browser and the sequences are held in the page, so nothing is sent to a server.

Also searched as

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