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Fasta format file input

AlexanderGress edited this page Nov 12, 2021 · 1 revision

To annotate proteins, whose sequences are stored in the online resource that are supported by StructMAn, one can provide any input in fasta-format files.
The header lines for each protein sequence should be in the following format:
>[Some_protein_idnetifier_or_name]
The given identifiers may not contain whitespaces and need to be unique throughout the file. They are later used to trace the outputs. The header can have more optional inputs:
>[Some_protein_idnetifier_or_name] [One-letter code amino acid of wildtype][Position in the sequence][One-letter code amino acid of mutant]
In case, one wants to specify multiple positions or mutations, one can semi-colons:
>[Some_protein_idnetifier_or_name] [first mutation];[second mutation and so on]
One can also deliver arbitrary tags together with specific positions/mutations:
>[Some_protein_idnetifier_or_name] [mutation]<[some tag],[another tag]

Here an example file:

>A000082:1:BDH_HUMAN
MLATRLSRPLSRLPGKTLSACDRENGARRPLLLGSTSFIPIGRRTYASAAEPVGSKAVLV
TGCDSGFGFSLAKHLHSKGFLVFAGCLMKDKGHDGVKELDSLNSDRLRTVQLNVcSSEEV
EKVVEIVRSSLKDPEKGMWGLVNNAGISTFGEVEFTSLETYKQVAEVNLWGTVRMTKSFL
PLIRRAKGRVVNISSMLGRMANPARSPYCITKFGVEAFSDCLRYEMYPLGVKVSVVEPGN
FIAATSLYSPESIQAIAKKMWEELPEVVRKDYGKKYFDEKIAKMETYcSSGSTDTSPVID
AVTHALTATTPYTRYHPMDYYWWLRMQIMTHLPGAISDMIYIR//
>A000195:2:AAPK2_RAT T172D
MAEKQKHDGRVKIGHYVLGDTLGVGTFGKVKIGEHQLTGHKVAVKILNRQKIRSLDVVGK
IKREIQNLKLFRHPHIIKLYQVISTPTDFFMVMEYVSGGELFDYICKHGRVEEVEARRLF
QQILSAVDYCHRHMVVHRDLKPENVLLDAQMNAKIADFGLSNMMSDGEFLRtSCGSPNYA
APEVISGRLYAGPEVDIWSCGVILYALLCGTLPFDDEHVPTLFKKIRGGVFYIPEYLNRS
IATLLMHMLQVDPLKRATIKDIREHEWFKQDLPSYLFPEDPSYDANVIDDEAVKEVCEKF
ECTESEVMNSLYSGDPQDQLAVAYHLIIDNRRIMNQASEFYLASSPPTGSFMDDMAMHIP
PGLKPHPERMPPLIADSPKARCPLDALNTTKPKSLAVKKAKWHLGIRSQSKPYDIMAEVY
RAMKQLDFEWKVVNAYHLRVRRKNPVTGNYVKMSLQLYLVDNRSYLLDFKSIDDEVVEQR
SGSSTPQRSCSAAGLHRPRSSVDSSTAENHSLSGSLTGSLTGSTLSSASPRLGSHTMDFF
EMCASLITALAR//
>A000274:1:ACTP_ACACA K108<tag_example;K106E<tag_example,second_tag
MSGIAVSDDCVQKFNELKLGHQHRYVTFKMNASNTEVVVEHVGGPNATYEDFKSQLPERD
CRYAIFDYEFQVDGGQRNKITFILWAPDSAPIkSkMMYTSTkdSIkkkLVGIQVEVQATD
AAEISEDAVSERAKKDVK//
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