trRosetta: protein structure prediction with transform-restrained Rosetta

Available multiple sequence alignment formats

The trRosetta server now supports using a multiple sequence alignment as input. Available formats for the input multiple sequence alignment are:

A3M
FASTA
A2M
STO

A3M format

The A3M format consists of aligned fasta, in which alignments are shown with inserts as lower case characters, matches as upper case characters, deletions as ' - ', and gaps aligned to inserts as ' . '. Note that gaps aligned to inserts can be omitted in the A3M format.

In the standard A3M format, sequences are separated by ' > '. See an example:

>example ETESMKTVRIREKIKKFLGDRPRNTAEILEHINSTMRHGTTSQQLGNVLSKDKDIVKVGYIKRSGILSGGYDICEWATRNWVAEHCPEWTE >1 ----MRTTRLRQKIKKFLNERGeANTTEILEHVNSTMRHGTTPQQLGNVLSKDKDILKVATTKRGGALSGRYEICVWTLRP----------- >2 ----MDSQNLRDLIRNYLSERPRNTIEISAWLASQMDPNSCPEDVTNILEADESIVRIGTVRKSGMRLTDLPISEWASSSWVRRHE----- >3 ----MNSQNLRELIRNYLSERPRNTIEISTWLSSQIDPTNSPVDITSILEADDQIVRIGTVRKSGMRRSESPVSEWASNTWVKHHE----- >4 --RDMDTEKVREIVRNYISERPRNTAEIAAWLNRH-DDGTGGSDVAAILESDGSFVRIGTVRTSGMTGNSPPLSEWATEKWIQHHER---- >5 -----RTRRLREAVLVFLEEKGnANTVEVFDYLNERFRWGATMNQVGNILAKDTRFAKVGHQ-RGQFRGSVYTVCVWALS------------ >6 -----RTKRLREAVRVYLAENGrSHTVDIFDHLNDRFSWGATMNQVGNILAKDNRFEKVGHVRD-FFRGARYTVCVWDLAS-----------

The separator line can be omitted. In this case, each sequence should be written into one line. See an example:

ETESMKTVRIREKIKKFLGDRPRNTAEILEHINSTMRHGTTSQQLGNVLSKDKDIVKVGYIKRSGILSGGYDICEWATRNWVAEHCPEWTE ----MRTTRLRQKIKKFLNERGeANTTEILEHVNSTMRHGTTPQQLGNVLSKDKDILKVATTKRGGALSGRYEICVWTLRP----------- ----MDSQNLRDLIRNYLSERPRNTIEISAWLASQMDPNSCPEDVTNILEADESIVRIGTVRKSGMRLTDLPISEWASSSWVRRHE----- ----MNSQNLRELIRNYLSERPRNTIEISTWLSSQIDPTNSPVDITSILEADDQIVRIGTVRKSGMRRSESPVSEWASNTWVKHHE----- --RDMDTEKVREIVRNYISERPRNTAEIAAWLNRH-DDGTGGSDVAAILESDGSFVRIGTVRTSGMTGNSPPLSEWATEKWIQHHER---- -----RTRRLREAVLVFLEEKGnANTVEVFDYLNERFRWGATMNQVGNILAKDTRFAKVGHQ-RGQFRGSVYTVCVWALS------------ -----RTKRLREAVRVYLAENGrSHTVDIFDHLNDRFSWGATMNQVGNILAKDNRFEKVGHVRD-FFRGARYTVCVWDLAS-----------

FASTA format

The FASTA format consists of aligned fasta, in which lower and upper case are equivalent; ' . ' and ' - ' are equivalent.

In the standard FASTA format, sequences are separated by ' > '. See an example:

>example ETESMKTVRIREKIKKFLGDRPRNTAEILEHINSTMRHGTTSQQLGNVLSKDKDIVKVGYIKRSGILSGGYDICEWATRNWVAEHCPEWTE >1 ----MRTTRLRQKIKKFLNERGANTTEILEHVNSTMRHGTTPQQLGNVLSKDKDILKVATTKRGGALSGRYEICVWTLRP----------- >2 ----MDSQNLRDLIRNYLSERPRNTIEISAWLASQMDPNSCPEDVTNILEADESIVRIGTVRKSGMRLTDLPISEWASSSWVRRHE----- >3 ----MNSQNLRELIRNYLSERPRNTIEISTWLSSQIDPTNSPVDITSILEADDQIVRIGTVRKSGMRRSESPVSEWASNTWVKHHE----- >4 --RDMDTEKVREIVRNYISERPRNTAEIAAWLNRH-DDGTGGSDVAAILESDGSFVRIGTVRTSGMTGNSPPLSEWATEKWIQHHER---- >5 -----RTRRLREAVLVFLEEKGANTVEVFDYLNERFRWGATMNQVGNILAKDTRFAKVGHQ-RGQFRGSVYTVCVWALS------------ >6 -----RTKRLREAVRVYLAENGSHTVDIFDHLNDRFSWGATMNQVGNILAKDNRFEKVGHVRD-FFRGARYTVCVWDLAS-----------

The separator line can be omitted. In this case, each sequence should be written into one line. See an example:

ETESMKTVRIREKIKKFLGDRPRNTAEILEHINSTMRHGTTSQQLGNVLSKDKDIVKVGYIKRSGILSGGYDICEWATRNWVAEHCPEWTE ----MRTTRLRQKIKKFLNERGANTTEILEHVNSTMRHGTTPQQLGNVLSKDKDILKVATTKRGGALSGRYEICVWTLRP----------- ----MDSQNLRDLIRNYLSERPRNTIEISAWLASQMDPNSCPEDVTNILEADESIVRIGTVRKSGMRLTDLPISEWASSSWVRRHE----- ----MNSQNLRELIRNYLSERPRNTIEISTWLSSQIDPTNSPVDITSILEADDQIVRIGTVRKSGMRRSESPVSEWASNTWVKHHE----- --RDMDTEKVREIVRNYISERPRNTAEIAAWLNRH-DDGTGGSDVAAILESDGSFVRIGTVRTSGMTGNSPPLSEWATEKWIQHHER---- -----RTRRLREAVLVFLEEKGANTVEVFDYLNERFRWGATMNQVGNILAKDTRFAKVGHQ-RGQFRGSVYTVCVWALS------------ -----RTKRLREAVRVYLAENGSHTVDIFDHLNDRFSWGATMNQVGNILAKDNRFEKVGHVRD-FFRGARYTVCVWDLAS-----------

A2M format

The A2M format consists of aligned fasta, in which alignments are shown with inserts as lower case characters, matches as upper case characters, deletions as ' - ', and gaps aligned to inserts as ' . '.

In the standard A2M format, sequences are separated by ' > '. See an example:

>example ETESMKTVRIREKIKKFLGDRP.RNTAEILEHINSTMRHGTTSQQLGNVLSKDKDIVKVGYIKRSGILSGGYDICEWATRNWVAEHCPEWTE >1 ----MRTTRLRQKIKKFLNERGeANTTEILEHVNSTMRHGTTPQQLGNVLSKDKDILKVATTKRGGALSGRYEICVWTLRP----------- >2 ----MDSQNLRDLIRNYLSERP.RNTIEISAWLASQMDPNSCPEDVTNILEADESIVRIGTVRKSGMRLTDLPISEWASSSWVRRHE----- >3 ----MNSQNLRELIRNYLSERP.RNTIEISTWLSSQIDPTNSPVDITSILEADDQIVRIGTVRKSGMRRSESPVSEWASNTWVKHHE----- >4 --RDMDTEKVREIVRNYISERP.RNTAEIAAWLNRH-DDGTGGSDVAAILESDGSFVRIGTVRTSGMTGNSPPLSEWATEKWIQHHER---- >5 -----RTRRLREAVLVFLEEKGnANTVEVFDYLNERFRWGATMNQVGNILAKDTRFAKVGHQ-RGQFRGSVYTVCVWALS------------ >6 -----RTKRLREAVRVYLAENGrSHTVDIFDHLNDRFSWGATMNQVGNILAKDNRFEKVGHVRD-FFRGARYTVCVWDLAS-----------

The separator line can be omitted. In this case, each sequence should be written into one line. See an example:

ETESMKTVRIREKIKKFLGDRP.RNTAEILEHINSTMRHGTTSQQLGNVLSKDKDIVKVGYIKRSGILSGGYDICEWATRNWVAEHCPEWTE ----MRTTRLRQKIKKFLNERGeANTTEILEHVNSTMRHGTTPQQLGNVLSKDKDILKVATTKRGGALSGRYEICVWTLRP----------- ----MDSQNLRDLIRNYLSERP.RNTIEISAWLASQMDPNSCPEDVTNILEADESIVRIGTVRKSGMRLTDLPISEWASSSWVRRHE----- ----MNSQNLRELIRNYLSERP.RNTIEISTWLSSQIDPTNSPVDITSILEADDQIVRIGTVRKSGMRRSESPVSEWASNTWVKHHE----- --RDMDTEKVREIVRNYISERP.RNTAEIAAWLNRH-DDGTGGSDVAAILESDGSFVRIGTVRTSGMTGNSPPLSEWATEKWIQHHER---- -----RTRRLREAVLVFLEEKGnANTVEVFDYLNERFRWGATMNQVGNILAKDTRFAKVGHQ-RGQFRGSVYTVCVWALS------------ -----RTKRLREAVRVYLAENGrSHTVDIFDHLNDRFSWGATMNQVGNILAKDNRFEKVGHVRD-FFRGARYTVCVWDLAS-----------

STO format

The STO (Stockholm) format consists of a header line with a format and version identifier; mark-up lines starting with "#=GF","#=GC","#=GS" or "#=GR"; alignment lines with the sequence name and aligned sequence; a "//" line indicating the end of the alignment. Alignments are shown with inserts as lower case characters, matches as upper case characters, and gaps as ' . ' or ' - '.

See an example:

# STOCKHOLM 1.0 #=GF ID DUF3860 #=GF AC PF12976.9 #=GF DE Domain of Unknown Function with PDB structure (DUF3860) #=GF AU Ellrott K;0000-0002-6573-5900 #=GF SE JCSG structure PDB:2OD5 #=GF GA 27.00 27.00; #=GF TC 33.80 46.10; #=GF NC 26.00 21.70; #=GF BM hmmbuild HMM.ann SEED.ann #=GF SM hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq #=GF TP Family #=GF WK Domain_of_unknown_function #=GF CL CL0123 #=GF DR INTERPRO; IPR024619; #=GF DR SO; 0100021; polypeptide_conserved_region; #=GF CC A protein family created to cover PDB:2OD5. 2OD5 is a #=GF CC hypothetical protein (JCVI_PEP_1096688149193) from an #=GF CC environmental metagenome (unidentified marine microbe). #=GF SQ 2 #=GS A0A3A5W886_9EURY/2-78 AC A0A3A5W886.1 #=GS A0A3A5W7Z0_9EURY/1-90 AC A0A3A5W7Z0.1 A0A3A5W886_9EURY/2-78 s-RTARLRNEIAQYLETNgVSNTSQILDHVNKRFRWGATMNQVGNVLARDRRFEKLGITEGTTMAGFRERVCIWA-------------------lva A0A3A5W7Z0_9EURY/1-90 .MKTVRIREKIKKFLGDK.PRNTAEILEHINSTMRHGTTSQQLGNVLSKDKDIVKVGYIKRSGILSGGYDICEWATRTWVS-DNCPGWEEG---qp. #=GC seq_cons ..+TsRlRpcItpaLtsp.spNTupIL-HlNpphRaGsT.pQlGNVLu+D+ch.KlGhhctoshhuht.clC.WA....................s. //

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