So I have about 5-10 samples of DNA from which I amplified one specific exon that was targeted to create a mutant cell line. These samples are single-allele sequences that were obtained by performing a TOPO-TA cloning reaction (transforming e coli with plasmids containing the amplicon = the exon in question).
What I am wondering is how do I present my results in a paper? I have used alignments softwares such as the Ensembl BLAT function and the NCBI BLASTn function to analyse the mutations in the sequenced samples against the WT sequence of the Exon, but I'm not sure how to present my results. The exon in question is quite short, and I'm only really interested in a 20 bp section, so I was thinking of just typing out the WT exon sequence and then underneath typing the relevant exon sequences I have obtained from my samples, and highlighting each nucleotide with a different colour and inserting "-" where deletions have occurred. So this would make for a pretty colourful image, but easy enough to interpret I think. I am not really able to find any relevant examples of how to present such data in literature. Do you think this is appropriate? Or is there perhaps a better way of showing this? Thank you very much for any help!
There are lots of web based tools that will generate multiple sequence alignments for you, just search on that term and you will find. Even BLAST has a multiple aligner.
Obviously if you do it in a word processor (since as you say these are fairly short and not too many) you can choose how to present in terms of colors or other such way to highlight. Be sure to use a Fixed width font though.
Hello Michael,
You may have a look at the following published articles (the titles given below) and get an idea for MSA representation in your paper:
1) Oxidative Stress Responsive SERK1 Gene Directs the Progression of Somatic Embryogenesis in Cotton (Gossypium hirsutum L. cv. Coker 310)
2) Genome-wide Analysis of LBD (LATERAL ORGAN BOUNDARIES Domain) Gene Family in Brassica rapa
3) Scaffold protein GhMORG1 enhances the resistance of cotton to Fusarium oxysporum by facilitating the MKK6‐MPK4 cascade
4)SARS-CoV-2 ORF8 and SARS-CoV ORF8ab: Genomic Divergence and Functional Convergence
Hope it helps and gives you an idea.
Michael J. Benedik Thank you for your help. I remember trying to align the sequences on NCBI BLASTn, but it gave the sequences aligned in bits, meaning it just gave me multiple bits of aligned sequences but not all aligned together, just in pairs, which is basically what you get when you align them separately anyways.
And also, what do you mean by "fixed width font"?
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