Multiple Sequence Alignment(MSA)格式详解

介绍

在生物信息学中，同源搜索，多序列比对等都是常用的方式，但是有很多的软件可以实现这些同源搜索和多序列比对，但是不同的软件输出的文件格式却是不完全一致，有熟悉的FASTA格式的，也有A2M, A3M等格式，虽然他们都是MSA文件但是对齐的规则却非常的不一致，本篇文章主要是介绍一下这三个格式之间的对齐规则差异。

FASTA

样式

>d1a1x__ b.63.1.1 (-) p13-MTCP1 {Human (Homo sapiens)}
PPDHLWVHQEGIYRDEYQRTWVAVVEE--E--T--SF---------LR----------ARVQQIQVPLG-------DAARPSHLLTS-----QL
>gi|6678257|ref|NP_033363.1|:(7-103) T-cell lymphoma breakpoint 1 [Mus musculus]
HPNRLWIWEKHVYLDEFRRSWLPVVIK--S--N--EK---------FQ----------VILRQEDVTLG-------EAMSPSQLVPY-----EL
>gi|7305557|ref|NP_038800.1|:(8-103) T-cell leukemia/lymphoma 1B, 3 [Mus musculus]
PPRFLVCTRDDIYEDENGRQWVVAKVE--T--S--RSpygsrietcIT----------VHLQHMTTIPQ-------EPTPQQPINNN-----SL
>gi|11415028|ref|NP_068801.1|:(2-106) T-cell lymphoma-1; T-cell lymphoma-1A [Homo sapiens]
HPDRLWAWEKFVYLDEKQHAWLPLTIEikD--R--LQ---------LR----------VLLRREDVVLG-------RPMTPTQIGPS-----LL
>gi|7305561|ref|NP_038804.1|:(7-103) T-cell leukemia/lymphoma 1B, 5 [Mus musculus]
----------GIYEDEHHRVWIAVNVE--T--S--HS---------SHgnrietcvt-VHLQHMTTLPQ-------EPTPQQPINNN-----SL
>gi|7305553|ref|NP_038801.1|:(5-103) T-cell leukemia/lymphoma 1B, 1 [Mus musculus]
LPVYLVSVRLGIYEDEHHRVWIVANVE--TshS--SH---------GN----------RRRTHVTVHLW-------KLIPQQVIPFNplnydFL
>gi|27668591|ref|XP_234504.1|:(7-103) similar to Chain A, Crystal Structure Of Murine Tcl1
-PDRLWLWEKHVYLDEFRRSWLPIVIK--S--N--GK---------FQ----------VIMRQKDVILG-------DSMTPSQLVPY-----EL
>gi|27668589|ref|XP_234503.1|:(9-91) similar to T-cell leukemia/lymphoma 1B, 5;
-PHILTLRTHGIYEDEHHRLWVVLDLQ--A--ShlSF---------SN----------RLLIYLTVYLQqgvafplESTPPSPMNLN-----GL
>gi|7305559|ref|NP_038802.1|:(8-102) T-cell leukemia/lymphoma 1B, 4 [Mus musculus] 
PPCFLVCTRDDIYEDEHGRQWVAAKVE--T--S--SH---------SPycskietcvtVHLWQMTTLFQ-------EPSPDSLKTFN-----FL
>gi|7305555|ref|NP_038803.1|:(9-102) T-cell leukemia/lymphoma 1B, 2 [Mus musculus]
---------PGFYEDEHHRLWMVAKLE--T--C--SH---------SPycnkietcvtVHLWQMTRYPQ-------EPAPYNPMNYN-----FL

对齐规则

匹配(Match)：  大写字母
插入(Insert)： 字母
删除(Delete)： -
补位(Gap)：    -

A2M

样式

>d1a1x__ b.63.1.1 (-) p13-MTCP1 {Human (Homo sapiens)}
PPDHLWVHQEGIYRDEYQRTWVAVVEE..E..T..SF.........LR..........ARVQQIQVPLG.......DAARPSHLLTS.....QL
>gi|6678257|ref|NP_033363.1|:(7-103) T-cell lymphoma breakpoint 1 [Mus musculus]
HPNRLWIWEKHVYLDEFRRSWLPVVIK..S..N..EK.........FQ..........VILRQEDVTLG.......EAMSPSQLVPY.....EL
>gi|7305557|ref|NP_038800.1|:(8-103) T-cell leukemia/lymphoma 1B, 3 [Mus musculus]
PPRFLVCTRDDIYEDENGRQWVVAKVE..T..S..RSpygsrietcIT..........VHLQHMTTIPQ.......EPTPQQPINNN.....SL
>gi|11415028|ref|NP_068801.1|:(2-106) T-cell lymphoma-1; T-cell lymphoma-1A [Homo sapiens]
HPDRLWAWEKFVYLDEKQHAWLPLTIEikD..R..LQ.........LR..........VLLRREDVVLG.......RPMTPTQIGPS.....LL
>gi|7305561|ref|NP_038804.1|:(7-103) T-cell leukemia/lymphoma 1B, 5 [Mus musculus]
----------GIYEDEHHRVWIAVNVE..T..S..HS.........SHgnrietcvt.VHLQHMTTLPQ.......EPTPQQPINNN.....SL
>gi|7305553|ref|NP_038801.1|:(5-103) T-cell leukemia/lymphoma 1B, 1 [Mus musculus]
LPVYLVSVRLGIYEDEHHRVWIVANVE..TshS..SH.........GN..........RRRTHVTVHLW.......KLIPQQVIPFNplnydFL
>gi|27668591|ref|XP_234504.1|:(7-103) similar to Chain A, Crystal Structure Of Murine Tcl1
-PDRLWLWEKHVYLDEFRRSWLPIVIK..S..N..GK.........FQ..........VIMRQKDVILG.......DSMTPSQLVPY.....EL
>gi|27668589|ref|XP_234503.1|:(9-91) similar to T-cell leukemia/lymphoma 1B, 5;
-PHILTLRTHGIYEDEHHRLWVVLDLQ..A..ShlSF.........SN..........RLLIYLTVYLQqgvafplESTPPSPMNLN.....GL
>gi|7305559|ref|NP_038802.1|:(8-102) T-cell leukemia/lymphoma 1B, 4 [Mus musculus] 
PPCFLVCTRDDIYEDEHGRQWVAAKVE..T..S..SH.........SPycskietcvtVHLWQMTTLFQ.......EPSPDSLKTFN.....FL
>gi|7305555|ref|NP_038803.1|:(9-102) T-cell leukemia/lymphoma 1B, 2 [Mus musculus]
---------PGFYEDEHHRLWMVAKLE..T..C..SH.........SPycnkietcvtVHLWQMTRYPQ.......EPAPYNPMNYN.....FL

对齐规则

匹配(Match)：  大写字母
插入(Insert)： 小写字母
删除(Delete)： -
补位(Gap)：    .

A3M

样式

>d1a1x__ b.63.1.1 (-) p13-MTCP1 {Human (Homo sapiens)}
PPDHLWVHQEGIYRDEYQRTWVAVVEEETSFLRARVQQIQVPLGDAARPSHLLTSQL
>gi|6678257|ref|NP_033363.1|:(7-103) T-cell lymphoma breakpoint 1 [Mus musculus]
HPNRLWIWEKHVYLDEFRRSWLPVVIKSNEKFQVILRQEDVTLGEAMSPSQLVPYEL
>gi|7305557|ref|NP_038800.1|:(8-103) T-cell leukemia/lymphoma 1B, 3 [Mus musculus]
PPRFLVCTRDDIYEDENGRQWVVAKVETSRSpygsrietcITVHLQHMTTIPQEPTPQQPINNNSL
>gi|11415028|ref|NP_068801.1|:(2-106) T-cell lymphoma-1; T-cell lymphoma-1A [Homo sapiens]
HPDRLWAWEKFVYLDEKQHAWLPLTIEikDRLQLRVLLRREDVVLGRPMTPTQIGPSLL
>gi|7305561|ref|NP_038804.1|:(7-103) T-cell leukemia/lymphoma 1B, 5 [Mus musculus]
----------GIYEDEHHRVWIAVNVETSHSSHgnrietcvtVHLQHMTTLPQEPTPQQPINNNSL
>gi|7305553|ref|NP_038801.1|:(5-103) T-cell leukemia/lymphoma 1B, 1 [Mus musculus]
LPVYLVSVRLGIYEDEHHRVWIVANVETshSSHGNRRRTHVTVHLWKLIPQQVIPFNplnydFL
>gi|27668591|ref|XP_234504.1|:(7-103) similar to Chain A, Crystal Structure Of Murine Tcl1
-PDRLWLWEKHVYLDEFRRSWLPIVIKSNGKFQVIMRQKDVILGDSMTPSQLVPYEL
>gi|27668589|ref|XP_234503.1|:(9-91) similar to T-cell leukemia/lymphoma 1B, 5;
-PHILTLRTHGIYEDEHHRLWVVLDLQAShlSFSNRLLIYLTVYLQqgvafplESTPPSPMNLNGL
>gi|7305559|ref|NP_038802.1|:(8-102) T-cell leukemia/lymphoma 1B, 4 [Mus musculus] 
PPCFLVCTRDDIYEDEHGRQWVAAKVETSSHSPycskietcvtVHLWQMTTLFQEPSPDSLKTFNFL
>gi|7305555|ref|NP_038803.1|:(9-102) T-cell leukemia/lymphoma 1B, 2 [Mus musculus]
---------PGFYEDEHHRLWMVAKLETCSHSPycnkietcvtVHLWQMTRYPQEPAPYNPMNYNFL

对齐规则

匹配(Match)：  大写字母
插入(Insert)： 小写字母
删除(Delete)： -

A3M的格式是A2M的压缩版，只需要去掉A2M中的补位符(.)就是A3M了

参考

https://github.com/soedinglab/hh-suite/wiki#multiple-sequence-alignment-formats