Heatmap of motifs present in protein sequences

Question

I have a file containing multiple protein amino acid sequences. I am interested in visually presenting the location of amino acid motifs PQG, QQG and AQG in the sequence in the form of a heatmap in R. Every location of the motifs should be represented as a differently coloured barcode. Example sequence follows,

>cat archae.fasta
>A0A075FKY9
MRRITLPKGIEISGKSPFGTSSGVYEVVISISENKPSDASIASNSFNSLWKDNFHLRVSG
DHFSQVLGSGSNPIPDNVFDLGSVWIVIQDQFSPVHTSFQFNISPSNQPASKPEEKPRRV
ETSTVKRTITKPGRLGPPGGKGPRGPSGYPGIKGDKGGRGPTGDKGDKGDKGIPGPQGEK
GKTGQAGDKGDKGITGPPGEKGPRGSTGPPGDKGDKGVQGKIGDKGLTGTTGPVGDKGTQ
GPQGPPGGKGLTGIPGPQGDKGTKGPLGPVGERGPTGKPGESGLQGPQGIQGAQGERGHS
GPPGPQGEKGLIGDKGEIGERGTRGPPGPPGEKGSQGGMSDEGKRLIKELLELLASKNII
STEEQIKLTSYLY
>A0A075FMB0
MPGDKGTSGIRGVPGDKGDKGPQGPPGDKGLTGPVGVPGEKGPTGTSGVQGEKGIQGTPG
PLGEKGVTGPAGDKGPIGPPGPAGSKGITGPAGPLGDKGTIGPPGPLGDKGSKGPEGPTG
DKGPQGPQGPAGAKGLTGVPGPQGEKGEKGPLGPIGEKGTTGATGPPGDKGPQGPQGTQG
ERGTTGPSGEKGPQGPQGIQGPQGERGPTGPIGSIGETGPIGGQGPVGPAGPRGPPGPPG
EKGPSGGMSSEQKAIFKELLEILTTKEIISTEEQIKLMSYLY
>A0A075G2F8
MPKGIEISGKSPFGTSSGVYEVKISVSQSKPSNDSITNNSFNSLWKDNFHLRVSEGYFSE
ILGSDSNPIPDNVFDLGSVWIVIQDQFSPVHTSFEFKISQDSKSIPTPKEKPRRVDTSSV
KKVRTIPTRQGPTGSKGIPGERGYPGTKGEKGGKGPTGDKGDKGDKGVPGPQGEKGKTGS
TGDKGDKGITGSPGEKGPRGPTGPPGDKGDKGVQGKIGDKGLTGTTGPIGDKGPQGPQGP
PGDKGLTGIPGPQGDKGGRGTIGPSGERGPTGRPGESGLQGPQGIQGPQGERGHSGPPGP
QGEKGIIGDKGEIGERGPRGPPGPPGEKGSQGGMSDDGKILFKELLQLLASKNIISTEEQ
IKLTSYLY
>A0A075GLR7
MPKGIEISGKSPFGTSSGVYEVRISISQDKPSDDGITNNSFNSLWKDNFHLRVSEGHFSE
ILGTDSNPIPADVFGLGSIWIIIQDQFSPVHTSFELHISQDNKLLSVPQGKPKPVNATKV
QKVRAQPGRPGPQGEKGGKGPAGYPGTRGEKGGRGITGDKGDKGDKGIPGPQGEKGIKGP
AGDKGDKGITGPVGPSGPKGSTGPPGDKGDKGVQGKSGDKGLTGVTGPLGDKGTQGPQGP
PGPKGLTGVPGPQGDKGMRGSIGPAGERGPTGKPGDPGLPGPQGIQGPQGERGHTGPQGP
PGEKGLVGDKGEIGDRGPRGPPGPPGEKGSQGGMSEESKRLVKELLELLASKNIISTEEQ
IKLTSYLY

As an example, please see a two-colour heatmap. I need something similar but with three colours corresponding to each of the three motifs.

I looked at the heatmaply package but the biggest problem is that my matrix is not numeric. Is there way to make heatmap using text strings in R?

Motif is defined as any three character string that matches the general pattern either PQG, QQG and AQG in the uploaded sequence. y-axis is the fasta code appended after > (A0A075FKY9 for example). x-axis would depend on how the data is converted into a matrix.

Answer 1

Firstly, the problem with your data is that it ain't aligned. Without that your motif positions are not relative from one protein to another. Basically you need to align it and there's no wriggle room.

Secondly, its easy you simply parse the motifs you want and their location within the string - after it is aligned. In Python you would use finditer within a comprehension. This will go into a dataframe and subject to a heatmap package, I'm not a 'heatmap' person but it would be easy to graph where the x axis is the position where each motif is found and a qualitative score given for each type of motif (1-3 here). I don't know the equivalent in R.

There is an issue whether an indel will remove a motif and you would need to check for that by running the same command against an unaligned protein and seeing if the frequency matches.

My advice is to ask a new question with some code. I dunno whether someone has coded this already, - its easy to do. Personally, I don't think there's sufficient requirement, but I could be wrong.