Using hmm for protein profile analysis - Error using swalign

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Hi,

I have been trying to get the next alignment but Matlab says that there is an Error using swalign Both sequences must be amino acids, use ALPHABET = 'NT' for aligning nucleotides. I have looked for solutions here in the community (I found similars) but both of my sequences are amino acids and have the correct aminoacids.

hmm_7m = pfamhmmread('pf00002.ls')

hmm_7m =

struct with fields:

Name: '7tm_2'

PfamAccessionNumber: 'PF00002.15'

ModelDescription: '7 transmembrane receptor (Secretin family)'

ModelLength: 293

Alphabet: 'AA'

MatchEmission: [293×20 double]

InsertEmission: [293×20 double]

NullEmission: [0.0755 0.0516 0.0453 0.0530 0.0170 0.0402 0.0632 0.0684 0.0224 … ]

BeginX: [294×1 double]

MatchX: [292×4 double]

InsertX: [292×2 double]

DeleteX: [292×2 double]

FlankingInsertX: [2×2 double]

LoopX: [2×2 double]

NullX: [2×1 double]

>> load('gpcrfam.mat','hmm_7tm','seed_seqs')

>> seqdisp(seed_seqs([1 2 3]),'row',70)

ans =

23×81 char array

'>VIPR2_HUMAN/123-371 '

' 1 YILVKAIYTL GYSVS.LMSL ATGSIILCLF .RKLHCTR.N YIHLNLFLSF ILRAISVLVK .DDVLYSSS.'

' 71 GTLHCPD... .......... .......... ....QPSSW. ..V.GCKLSL VFLQYCIMAN FFWLLVEGLY'

'141 LHTLLVA... ...MLPP.RR CFLAYLLIGW GLPTVCIGAW TAAR...... .........L YLED......'

'211 ......TGC. WDTN.DHSVP W....WVIRI PILISIIVNF VLFISIIRIL LQKLT..... .SPDVGGNDQ'

'281 SQY....... .......... .......... ....KRLAKS TLLLIPLFGV HYMV..FAVF PISI...S.S'

'351 KYQILFELCL GSF....QGL VV '

' '

'>VIPR_CARAU/100-348 '

' 1 FRSVKIGYTI GHSVS.LISL TTAIVILCMS .RKLHCTR.N YIHMHLFVSF ILKAIAVFVK .DAVLYDVIQ'

' 71 ESDNCS.... .......... .......... .....TASV. ....GCKAVI VFFQYCIMAS FFWLLVEGLY'

'141 LHALLAVS.. ...FFSE.RK YFWWYILIGW GGPTIFIMAW SFAK...... .........A YFND......'

'211 ......VGC. WDIIENSDLF W....WIIKT PILASILMNF ILFICIIRIL RQKIN..... .CPDIGRNES'

'281 NQY....... .......... .......... ....SRLAKS TLLLIPLFGI NFII..FAFI PENI...K.T'

'351 ELRLVFDLIL GSF....QGF VV '

' '

'>VIPR1_RAT/140-386 '

' 1 YNTVKTGYTI GYSLS.LASL LVAMAILSLF .RKLHCTR.N YIHMHLFMSF ILRATAVFIK .DMALFNSG.'

' 71 EIDHCS.... .......... .......... .....EASV. ....GCKAAV VFFQYCVMAN FFWLLVEGLY'

'141 LYTLLAVS.. ...FFSE.RK YFWGYILIGW GVPSVFITIW TVVR...... .........I YFED......'

'211 ......FGC. WDTI.INSSL W....WIIKA PILLSILVNF VLFICIIRIL VQKLR..... .PPDIGKNDS'

'281 SPY....... .......... .......... ....SRLAKS TLLLIPLFGI HYVM..FAFF PDNF...K.A'

'351 QVKMVFELVV GSF....QGF VV '

>> seqs = strrep({seed_seqs.Sequence},'.', ' ');

names = {seed_seqs.Header};

>> fprintf('.')

scores=zeros(numel(seqs),1);

aligned_seqs=cell(numel(seqs),1);

for sn=1:numel(seqs)

fprintf('.')

[scores(sn),aligned_seqs{sn}]=hmmprofalign(hmm_7tm,seqs{sn});

end

fprintf('\n')

.................................

>> hmmprofmerge(aligned_seqs,names,scores)

>> str=hmmprofmerge(aligned_seqs);

str(1:10,1:80)

ans =

10×80 char array

'YILVKAIYTLGYSVS.LMSLATGSIILCLF.RKLHCTR.NYIHLNLFLSFILRAISVLVK.DDVLYSSSG-TLH......'

'FRSVKIGYTIGHSVS.LISLTTAIVILCMS.RKLHCTR.NYIHMHLFVSFILKAIAVFVK.DAVLYDVIQESDN......'

'YNTVKTGYTIGYSLS.LASLLVAMAILSLF.RKLHCTR.NYIHMHLFMSFILRATAVFIK.DMALFNSG-EIDH......'

'FGAIKTGYTIGHSLS.LISLTAAMIILCIF.RKLHCTR.NYIHMHLFMSFIMRAIAVFIK.DIVLFESG-ESDH......'

'YLSVKALYTVGYSTS.LVTLTTAMVILCRF.RKLHCTR.NFIHMNLFVSFMLRAISVFIK.DWILYAEQD-SSH......'

'FSTVKIIYTTGHSIS.IVALCVAIAILVAL.RRLHCPR.NYIHTQLFATFILKASAVFLK.DAAIFQGDS-TDH......'

'LSTLKQLYTAGYATS.LISLITAVIIFTCF.RKFHCTR.NYIHINLFVSFILRATAVFIK.DAVLFSDET-QNH......'

'FDRLGMIYTVGYSVS.LASLTVAVLILAYF.RRLHCTR.NYIHMHLFLSFMLRAVSIFVK.DAVLYSGATLDEA......'

'FERLYVMYTVGYSIS.FGSLAVAILIIGYF.RRLHCTR.NYIHMHLFVSFMLRATSIFVK.DRVVHAHIGVKEL......'

'ALNLFYLTIIGHGLS.IASLLISLGIFFYF.KSLSCQR.ITLHKNLFFSFVCNSVVTIIH.LTAVANNQALVAT......'

>> mousegpcr = getgenpept('NP_783573');

Bai3 = mousegpcr.Sequence;

>> load('gpcrfam.mat', 'mousegpcr')

Bai3 = mousegpcr.Sequence;

seqdisp(Bai3,'row',70)

ans =

22×82 char array

' 1 MKAVRNLLIY IFSTYLLVMF GFNAAQDFWC STLVKGVIYG SYSVSEMFPK NFTNCTWTLE NPDPTKYSIY'

' 71 LKFSKKDLSC SNFSLLAYQF DHFSHEKIKD LLRKNHSIMQ LCSSKNAFVF LQYDKNFIQI RRVFPTDFPG'

' 141 LQKKVEEDQK SFFEFLVLNK VSPSQFGCHV LCTWLESCLK SENGRTESCG IMYTKCTCPQ HLGEWGIDDQ'

' 211 SLVLLNNVVL PLNEQTEGCL TQELQTTQVC NLTREAKRPP KEEFGMMGDH TIKSQRPRSV HEKRVPQEQA'

' 281 DAAKFMAQTG ESGVEEWSQW SACSVTCGQG SQVRTRTCVS PYGTHCSGPL RESRVCNNTA LCPVHGVWEE'

' 351 WSPWSLCSFT CGRGQRTRTR SCTPPQYGGR PCEGPETHHK PCNIALCPVD GQWQEWSSWS HCSVTCSNGT'

' 421 QQRSRQCTAA AHGGSECRGP WAESRECYNP ECTANGQWNQ WGHWSGCSKS CDGGWERRMR TCQGAAVTGQ'

' 491 QCEGTGEEVR RCSEQRCPAP YEICPEDYLI SMVWKRTPAG DLAFNQCPLN ATGTTSRRCS LSLHGVASWE'

' 561 QPSFARCISN EYRHLQHSIK EHLAKGQRML AGDGMSQVTK TLLDLTQRKN FYAGDLLVSV EILRNVTDTF'

' 631 KRASYIPASD GVQNFFQIVS NLLDEENKEK WEDAQQIYPG SIELMQVIED FIHIVGMGMM DFQNSYLMTG'

' 701 NVVASIQKLP AASVLTDINF PMKGRKGMVD WARNSEDRVV IPKSIFTPVS SKELDESSVF VLGAVLYKNL'

' 771 DLILPTLRNY TVVNSKVIVV TIRPEPKTTD SFLEIELAHL ANGTLNPYCV LWDDSKSNES LGTWSTQGCK'

' 841 TVLTDASHTK CLCDRLSTFA ILAQQPREIV MESSGTPSVT LIVGSGLSCL ALITLAVVYA ALWRYIRSER'

' 911 SIILINFCLS IISSNILILV GQTQTHNKSI CTTTTAFLHF FFLASFCWVL TEAWQSYMAV TGKIRTRLIR'

' 981 KRFLCLGWGL PALVVATSVG FTRTKGYGTD HYCWLSLEGG LLYAFVGPAA AVVLVNMVIG ILVFNKLVSR'

'1051 DGILDKKLKH RAGQMSEPHS GLTLKCAKCG VVSTTALSAT TASNAMASLW SSCVVLPLLA LTWMSAVLAM'

'1121 TDKRSILFQI LFAVFDSLQG FVIVMVHCIL RREVQDAFRC RLRNCQDPIN ADSSSSFPNG HAQIMTDFEK'

'1191 DVDIACRSVL HKDIGPCRAA TITGTLSRIS LNDDEEEKGT NPEGLSYSTL PGNVISKVII QQPTGLHMPM'

'1261 SMNELSNPCL KKENTELRRT VYLCTDDNLR GADMDIVHPQ ERMMESDYIV MPRSSVSTQP SMKEESKMNI'

'1331 GMETLPHERL LHYKVNPEFN MNPPVMDQFN MNLDQHLAPQ EHMQNLPFEP RTAVKNFMAS ELDDNVGLSR'

'1401 SETGSTISMS SLERRKSRYS DLDFEKVMHT RKRHMELFQE LNQKFQTLDR FRDIPNTSSM ENPAPNKNPW'

'1471 DTFKPPSEYQ HYTTINVLDT EAKDTLELRP AEWEKCLNLP LDVQEGDFQT EV '

>> VIPR2 = seqs{1};

[sc_aa_affine, alignment] = swalign(Bai3, VIPR2,'ScoringMatrix', 'blosum30', 'gapopen',5,'extendgap',3,'showscore',true);

Bai3_aligned_region = strrep(alignment (1,:), '-', ' ');

Seqdotplot(VIPR2, Bai3_aligned_region,7,2)

ylabel('VIPR2'); xlabel('Bai3');

Error using swalign

Both sequences must be amino acids, use ALPHABET = 'NT' for aligning nucleotides.

Thats the hole code, i hope it works :(

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Answer 1

Walter Roberson 2023-4-8

在 MATLAB Online 中打开

0 个投票

swalign does not support '.' or '*'

It supports

*-ABCDEFGHIKLMNPQRSTVWXYZabcdefghiklmnpqrstvwxyz

together with '?' which is translated into X

('J' and 'O' and 'U' are not supported either)

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Walter Roberson 2023-4-8

在 MATLAB Online 中打开

hmm_7m = pfamhmmread('pf00002.ls')
load('gpcrfam.mat','hmm_7tm','seed_seqs')
seqdisp(seed_seqs([1 2 3]),'row',70)
seqs = strrep({seed_seqs.Sequence},'.', ' ');
names = {seed_seqs.Header};
fprintf('.')
scores=zeros(numel(seqs),1);
aligned_seqs=cell(numel(seqs),1);
for sn=1:numel(seqs)
fprintf('.')
[scores(sn),aligned_seqs{sn}]=hmmprofalign(hmm_7tm,seqs{sn});
end
fprintf('\n')
hmmprofmerge(aligned_seqs,names,scores)
str=hmmprofmerge(aligned_seqs);
str(1:10,1:80)
mousegpcr = getgenpept('NP_783573');
Bai3 = mousegpcr.Sequence;
load('gpcrfam.mat', 'mousegpcr')
Bai3 = mousegpcr.Sequence;
seqdisp(Bai3,'row',70)
VIPR2 = strrep(seqs{1}, ' ', 'X');
[sc_aa_affine, alignment] = swalign(Bai3, VIPR2,'ScoringMatrix', 'blosum30', 'gapopen',5,'extendgap',3,'showscore',true);
Bai3_aligned_region = strrep(alignment (1,:), '-', 'X');
seqdotplot(VIPR2, Bai3_aligned_region,7,2)
ylabel('VIPR2'); xlabel('Bai3');

Alan 2023-4-8

It works! tysm :)

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