Package: hiscan
Hiscan：Histone motif scanningHistone Motif Scan (HiScan) is a Python3-based character interface program that can be used and deployed on multiple systems including Windows, Linux and MacOS. This software is mainly used to quickly identify the presence of histone mimicry (HM) motifs in viral protein sequences.1. Download and installHiScan is developed viaPython 3, and you can get and install in following ways.HiScan has been distributed to the standard library pf PYPI, and can be easily installed by the toolpip.pip install hiscan
hiscan -h2. Getting helpYou can use "-h" or "--help" to get the help document. The following is a brief introduction to the each parameter of HiScan:ParameterDescription-h,--helpShow the help message and exit.-iThe file path of the viral protein sequence that needs for analysis in the file format "fasta". Supports input as a file or folder.-mrThe raw result of the viral protein sequence query for HM motifs is derived from the "-m" parameter result without any additional annotation information. The file format is "txt", "csv" or "xlsx", and the default is "txt".-nrThe result of viral protein sequence query of HM motifs, with NCBI species annotation information, derived from the "-na" parameter results, no host annotation information, file format is "txt", "csv" or "xlsx", default is "txt".-mHM motifs that need to be queried in viral protein sequences, file formats support "txt" and "xlsx".-naTo supplement the query results of NCBI species annotation information, input the NCBI protein annotation file (" gpff "format) path, support the form of file or folder input.-iaThe query results are supplemented with ICTV host annotation information, and the virus classification table path of ICTV is only supported in the form of a separate file, and this step must rely on the NCBI species annotation information, so it should be used after the "-na" parameter.-mcThe type and number of HM motifs in the raw result file will be counted and their occurrence frequency will be calculated.-msThe amino acid preference will be calculated based on the HM motif input file and the result will be saved in matrix form, while the HM motif combination with the highest probability will be given.-mpBased on the HM motif input file, all possible HM motif combinations will be calculated and their probabilities will be calculated simultaneously, and the number of motifs is recommended to be no more than 15.-ccBased on the raw file results, the number and frequency of the HM motifs included in each grade under the different classification criteria will be calculated. By default, "family" is used for statistics.-hcBased on the raw file results, the number and frequency of the occurrence of different host sources of the simulation motif will be calculated.-ctSpecify the classification level of the '-cc' parameter, which can be selected from 'Realm', 'Kingdom', 'Phylum', 'Class', 'Order', 'Family'.-oThe result file path.-onSpecify the name of the output file, default is "Result".-otSpecify the format of the output file, support "txt", "csv" and "xlsx" three formats of output, the default is "txt", recommended to use "xlsx" table format.3. Example of usage3.1 Raw material preparationYou will need to prepare a viral protein sequence file (required), a HM motif file (required), and protein annotation files (optional), in which the HM motif file content format should be as follows:[!NOTE]
You can download viral protein and its annotation information file from the NCBI database (https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/). The host annotation file is from the official website of ICTV (https://ictv.global/vmr), and HM motifs are from literature review. The following is an example of Windows platform operation.(1) No motif annotation informationJust the simple HM motif name without any additional information, note that the motif name should only be in the first column.Col-ACol-BLPKKTRGKQGGGKARRAKAK...(2) Motif with annotation informationThe format of the motif file with annotated information should be as follows, where the first column is the motif name, the second column is the subunit type of the histone, and the third column is the modification type of the motif. If the subunit type and modification type of some HM motifs are not clear, please replace them with the value "None" or a value. The rest of the annotation information is not currently supported.Col-ACol-BCol-CLPKKTH2AMethylationRGKQGH2AAcetylationGGKARH2AAcetylationKKTESH2APhosphorylationPAKSAH2BMethylation.........3.2 Obtaining raw resultCase 1: NCBI and ICTV annotation files are completeYou can refer to the following code, you need to input the viral protein sequence, HM motif file, NCBI and ICTV annotation file:hiscan -i your/viral_protein_file_path/ -m your/motif_path/ -na your/NCBI_annotation_path/ -ia your/ICTV_annotation_path -o your/result_path -ot result_formatThe output information is as follows:And your results should look like this：NCBI_IDSeq_NameMimicLocationHistone_SubunitModificationRealmKingdomPhylumClassOrderFamilySpeciesHost_SourceYP_009175074.1polyprotein [Bean rugose mosaic virus]LPKKT(1179:1183)H2AMethylationRiboviriaOrthornaviraePisuviricotaPisoniviricetesPicornaviralesSecoviridaeBean rugose mosaic virusplantsYP_009272812.1polyprotein [Washington bat picornavirus]LPKKT(969:973)H2AMethylationRiboviriaOrthornaviraePisuviricotaPisoniviricetesPicornaviralesPicornaviridaeWashington bat picornavirusNoneYP_009333551.1hypothetical protein 1 [Beihai picorna-like virus 85]LPKKT(438:442)H2AMethylationRiboviriaNoneNoneNoneNoneNoneBeihai picorna-like virus 85None..........................................Case 2: There is no annotation informationThere is no annotation information, and even the HM motif file has no additional information, at which point only the virus protein sequence file and the HM motif file need to be passed in:hiscan -i your/viral_protein_file_path/ -m your/motif_path/ -o your/result_pathYour results should look like the following:NCBI_IDSeq_NameMimicLocationYP_009175074.1polyprotein [Bean rugose mosaic virus]LPKKT(1179:1183)YP_009272812.1polyprotein [Washington bat picornavirus]LPKKT(969:973)YP_009333551.1hypothetical protein 1 [Beihai picorna-like virus 85]LPKKT(438:442)............Case 3: Supplement annotation information to raw resultIf the result file of case 2 is generated, the NCBI or ICTV annotation file or the self-written annotation file (in accordance with the gpff format of NCBI) is available, then the result file of case 2 can be followed for analysis.
The annotation information that complements NCBI is taken as an example below:hiscan -mr your/raw_result_path/ -na your/NCBI_annotation_file -o your/result_path3.3 Analysis of motif residue skewnessIf you want to calculate the skewness of the HM motifs, you just need to input the HM motif file, you can refer to the following code:hiscan -i your/motif_path/ -ms -o your/result_pathAnd your result should look like the following:Col_0Col_1Col_2Col_3Col_4('R', 0.15094)('G', 0.15094)('K', 0.75472)('Q', 0.09434)('G', 0.13208)('G', 0.13208)('G', 0.15094)('K', 0.75472)('A', 0.13208)('R', 0.03774)('R', 0.15094)('A', 0.16981)('K', 0.75472)('A', 0.13208)('K', 0.09434)('K', 0.11321)('A', 0.16981)('K', 0.75472)('T', 0.09434)('R', 0.03774)...............3.4 Predicting HM motifsIf you want to predict possible HM motifs, you need to input a file of HM motifs as a background, and HiScan will calculate all possible combinations of HM motifs and sort them by probability.hiscan -i your/motif_path/ -mp -o your/result_pathAnd your results should look like this：MimicProbabiliryAGKVT0.0020117850867AGKVL0.0020117850867VAKVT0.0013411900578......3.5 Other AnalysesIf you want to perform some additional analysis on the raw result, such as host origin statistics, motif statistics, and so on, you can refer to the following code:hiscan -i your/raw_result_path/ -mc -o your/result_pathAnd your results should look like this：MimicCountFrequencyARKSA5840.09211ATKAA4670.07366ARKST3000.04732SGRGK2810.04432GTKAV2700.04259VYKVL2240.03533.........