How to align multiple Sequences with one reference sequence?

Question

[David]

Hello,

I'm just now starting to work with bioinformatics tools for my bachelor thesis, so I hope someone on here is able to help me with a problem I encountered.

I want to look at the Galactinol synthase family in vitis vinifera. I found 12 members of the family on Platza, also I have two genes for Galactinol Synthases from a paper I found, and now I want so compare those 12 members to each of the two genes from the paper.

My thought was to do 2 alignments, each time using one of the sequences from the paper as a reference and then aligning the 12 members of the gene family to them, to check how similar they are.

But I just don´t find a way to do so. I hope someone here is able to help, many thanks in advance!

[liorglic]

As suggested by Michael, you can use one of several MSA tools. However, the choice depends on the downstream analyses you plan to run. What would you do once you have the MSA? What question are you trying to answer or what kind of information are you looking for?

[Dunois]

All you need to do is a multiple sequence alignment (MSA). Put all your sequences in one plain text file (a FASTA file, basically), and then supply this file as input to a MSA tool of your choice; e.g., MAFFT here: https://mafft.cbrc.jp/alignment/server/index.html.

Then you can take that output and supply it to something like msavisr() from seqvisr (https://github.com/vragh/seqvisr) to visualize the alignments. Here, you can select which ever sequence you prefer within the MSA as the reference so that all gaps, mismatches, and matches are calculated according to this sequence.

Answer 1

[Michael]

You should try a multiple-sequence alignment (MSA). The easiest way to get there is via Jalview. Download the software, load all your sequences into it, and run one of the different MSA methods (Muscle, ClustalO, Mafft) via the Web service - Alignment menu.