short peptide mapping to Multiple seq alignment (MSA)

Question

[dravinashvasait]

Hello all,

I have a set of short peptides (200) comprising 5-30 amino acids that l have to map (align) these peptides against MSA file order to detect polymorphisms present in short peptides. I tried fuzzpro (EMBOSS package) but it takes only one pattern (peptide seq) as input. Could you please recommend me some tools where I can give multiple peptides as input to map against multiple sequence alignment file?

[Joe]

This is a Question not a Forum (Forum's are for extended discussion where there may not be a particular or singular right answer). I've changed it for you this time but please bear it in mind for future posts.

[dravinashvasait]

@jrj.healey. Thank you. I shall keep it in mind for next post. Thank you.

Answer 1

[Joe]

You can use Clustal for this. It is possible to align sequences against an existing HMM profile or MSA.

Take a look at the --help from clustalo:

Sequence Input:
  -i, --in, --infile={<file>,-} Multiple sequence input file (- for stdin)
  --hmm-in=<file>           HMM input files
  --dealign                 Dealign input sequences
  --profile1, --p1=<file>   Pre-aligned multiple sequence file (aligned columns will be kept fix)
  --profile2, --p2=<file>   Pre-aligned multiple sequence file (aligned columns will be kept fix)
  --is-profile              disable check if profile, force profile (default no)
  -t, --seqtype={Protein, RNA, DNA} Force a sequence type (default: auto)
  --infmt={a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]} Forced sequence input file format (default: auto)

Particularly, you'll be interested in the --profile options.

Answer 2

[Elisabeth Gasteiger]

UniProt's PeptideSearch doesn't map peptides against a MSA, but can find exact peptide matches (multiple peptides can be entered simultaneously) in the UniProt Knowledgebase: https://www.uniprot.org/peptidesearch