Instructions for submitting queries
PON-P2 allows users to submit queries in three formats.
1) Identifier submission
2) Genomic submission
3) Sequence submission
Identifier submission
Protein or gene identifier(s) and variation(s) are required in fasta-like format.
Ensembl gene identifier, NCBI gene ID and UniProtKB/Swiss-Prot accession can be used as identifiers.
When using Ensembl or NCBI gene identifier(s), the variation(s) have to be mapped to the longest isoform of the gene.
The identifier should be preceded by greater than sign (>).
Only one variation should be placed in one line.
Multiple variations in a single protein or in multiple proteins can be submitted in a single query.
Alternatively, a file containing identifier(s) and variation(s) in the same format can be uploaded.
Example:
>ENSG00000165816 #Ensembl gene identifier
I75F #reference amino acid,position in the sequence(1 based),variant amino acid
V366M
>Q16518 #UniProtKB/Swiss-Prot accession identifier
P363T
R44Q
>151194 #NCBI gene identifier
T9N
P111Q
The variations in UniProtKB/Swiss-Prot accession and the longest isoform of NCBI gene are mapped to longest isoform of corresponding Ensembl gene.
If the variations could not be mapped, they are reported in error log file and we recomend users to submit these variations again using Sequence submission service.
Genomic submission
This format requires variation(s) at genomic level.
The users are required to submit chromosome number, chromosome location, strand, reference nucleotide and variant nucleotide in the format mentioned in the example below.
Each line should contain only one variation.
Users can either paste the variation(s) in the text box or upload a file containing the variation(s).
Example:
3:49044874,+1,C,T
11:108368994,-1,G,C
16:11363014,-1,A,G
Users can also upload a Variant Call Format (VCF) file directly using VCF file submission link.
PON-P2 filters non-synonymous variations from VCF file and makes predictions for them.
Note: The chromosome location and reference alleles have to be provided in reference to the Genome Reference Consortium human genome (build 37) (GRCh37).
Sequence submission
This format requires users to submit fasta-format amino acid sequence(s) and variation(s) corresponding to the sequence(s).
Each sequence should have a header line starting with greater than sign (>) followed by description.
The sequence in upper-case characters follows the header line.
No characters except the universal 20 amino acid codes are accepted in the sequence(s).
The variation(s) corresponding to a sequence should contain the same header line as the sequence.
Variation(s) follow the header line and only one variation is allowed per line.
The sequence(s) and variation(s) can be pasted in the correponding text-boxes or separate files containing sequence(s) and variation(s) can be submitted.
Example sequences:
>ADA_HUMAN
MAQTPAFDKPKVELHVHLDGSIKPETILYYGRRRGIALPANTAEGLLNVIGMDKPLTLPD
FLAKFDYYMPAIAGCREAIKRIAYEFVEMKAKEGVVYVEVRYSPHLLANSKVEPIPWNQA
EGDLTPDEVVALVGQGLQEGERDFGVKARSILCCMRHQPNWSPKVVELCKKYQQQTVVAI
DLAGDETIPGSSLLPGHVQAYQEAVKSGIHRTVHAGEVGSAEVVKEAVDILKTERLGHGY
HTLEDQALYNRLRQENMHFEICPWSSYLTGAWKPDTEHAVIRLKNDQANYSLNTDDPLIF
KSTLDTDYQMTKRDMGFTEEEFKRLNINAAKSSFLPEDEKRELLDLLYKAYGMPPSASAG
QNL
>Retinal pigment
MSIQVEHPAGGYKKLFETVEELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHL
FDGQALLHKFDFKEGHVTYHRRFIRTDAYVRAMTEKRIVITEFGTCAFPDPCKNIFSRFF
SYFRGVEVTDNALVNVYPVGEDYYACTETNFITKINPETLETIKQVDLCNYVSVNGATAH
PHIENDGTVYNIGNCFGKNFSIAYNIVKIPPLQADKEDPISKSEIVVQFPCSDRFKPSYV
HSFGLTPNYIVFVETPVKINLFKFLSSWSLWGANYMDCFESNETMGVWLHIADKKRKKYL
NNKYRTSPFNLFHHINTYEDNGFLIVDLCCWKGFEFVYNYLYLANLRENWEEVKKNARKA
PQPEVRRYVLPLNIDKADTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQ
INYQKYCGKPYTYAYGLGLNHFVPDRLCKLNVKTKETWVWQEPDSYPSEPIFVSHPDALE
EDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEVARAEVEINIPVTFHGLFKKS
Variation examples:
>ADA_HUMAN
R101H #reference amino acid,position in the sequence(1 based),variant amino acid
R101L
S291L
>Retinal pigment
G75R
R97P
Email:
Users are required to submit a valid email address where the results will be sent when they are ready.
How to cite?
Niroula A, Urolagin S, Vihinen M (2015) PON-P2: Prediction Method for Fast and Reliable Identification of Harmful Variants. PLoS ONE 10(2):e0117380.doi:10.1371/journal.pone.0117380
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