How to use Manipulate for protein sequence alignment?

Question

I have the sequence of a protein from Chain A and Chain B and I want to use Manipulate to show what parts of sequence are identical.

This is what I have:

With[{Length = Length[seqAlign]}, Manipulate[ Grid[{If[ListQ[#], Column[#, Frame -> All, Spacings -> 1], #] & /@ seqAlign[[x ;; x + shownSize]]}, Frame -> All], {x, 1, seqLength - shownSize, 1}] ]

How do I make the whole thing visible? The function receives as parameter the sequence alignment of 2 proteins.

Answer 1

I'm using as examples the mouse and human sequences for Rhodopsin (the protein in retinal rod cells that detects photons).

mouse = "MNGTEGPNFYVPFSNVTGVVRSPFEQPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYV\
TVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVL\
AIERYVVVCKPMSNFRFGENHAIMGVVFTWIMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNE\
SFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIFFLICWLPYASV\
AFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMLNKQFRNCMLTTLCCGKNPLGDDDASATASKTE\
TSQVAPA";
human = "MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYV\
TVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVL\
AIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNE\
SFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASV\
AFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTE\
TSQVAPA";

s = SequenceAlignment[mouse, human]

(* {MNGTEGPNFYVPFSN,{V,A},TGVVRSPFE,{Q,Y},
PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV,
{F,L},GGFT,{T,S},TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGV,
{V,A},FTW,{I,V},MALACAAPPL,{V,A},GWSRYIPEG,{M,L},
QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI,{V,I},
IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVI,{F,A},
FLICW,{L,V},PYASVAFYIFTHQGSNFGPIFMT,{L,I},PAFFAKS,
{SS,AA},IYNPVIYIM,{L,M},NKQFRNCMLTT,{L,I},CCGKNPLGDD,{D,E},ASAT,{A,V},SKTETSQVAPA} *)

Your method works to scroll through the alignment:

Manipulate[
 seqLength = Length[s];
 shownSize = 5;
 Grid[{If[ListQ[#], Column[#, Frame -> All, Spacings -> 1], #] & /@ 
    s[[x ;; x + shownSize]]}, Frame -> All], {x, 1, 
  seqLength - shownSize, 1}]

Or for a more traditional representation:

aln1 = "";
aln2 = "";
ident = "";
Do[{
  If[Length[n] == 0,
   {
    aln1 = aln1 <> n,
    aln2 = aln2 <> n,
    Do[ident = ident <> "*", {StringLength[n]}]
    },
   {
    While[StringLength[n[[1]]] != StringLength[n[[2]]], {
      If[StringLength[n[[1]]] < StringLength[n[[2]]], 
       n[[1]] = n[[1]] <> "-",
       n[[2]] = n[[2]] <> "-"]
      }],
    Do[ident = ident <> " ", {Max[Map[StringLength, n]]}],
    aln1 = aln1 <> n[[1]],
    aln2 = aln2 <> n[[2]]
    }
   ]
  }, {n, s}]

Manipulate[
 seqLength2 = StringLength[ident];
 shownSize2 = 40;
 Grid[Characters[{ident, aln1, aln2}][[All, n ;; n + shownSize2]]]
 , {n, 1, seqLength2 - shownSize2, 1}]