Protein sequence diversity is one of the major challenges in the design of diagnostic, prophylactic and therapeutic interventions against viruses. DiMA is a tool designed to facilitate the dissection of protein sequence diversity dynamics for viruses. DiMA provides a quantitative measure of sequence diversity by use of Shannon’s entropy, applied via a user-defined k-mer sliding window. Further, the entropy value is corrected for sample size bias by applying a statistical adjustment. Additionally, DiMA further interrogates the diversity by dissecting the entropy value at each k-mer position to various diversity motifs. The distinct k-mer sequences at each position are classified into the following motifs based on their incidence.
Moreover, the description line of the sequences in the alignment can be formatted for inclusion of meta-data that can be tagged to the diversity motifs. DiMA enables comparative diversity dynamics analysis, within and between proteins of a virus species, and proteomes of different viral species.
pip install dima-cli
dima-cli -i aligned_sequences.afa -o results.json
from dima import Dima
results = Dima(sequences="aligned_sequences.afa").run()
{
"sequence_count": 5,
"support_threshold": 30,
"low_support_count": 20,
"query_name": "Unknown Query",
"kmer_length": 9,
"average_entropy": 0.06854034285524647,
"highest_entropy": {
"position": 186,
"entropy": 1.3921472236645345
},
"results": [
{
"position": 1,
"low_support": "LS",
"entropy": 0.7219280948873623,
"support": 5,
"distinct_variants_count": 1,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 20.0,
"diversity_motifs": [
{
"sequence": "MSASKEIKS",
"count": 4,
"incidence": 80.0,
"motif_short": "I",
"motif_long": "Index",
"metadata": null
},
{
"sequence": "SAGVYMGNL",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
}
]
},
{
"position": 2,
"low_support": "LS",
"entropy": 0.7219280948873623,
"support": 5,
"distinct_variants_count": 1,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 20.0,
"diversity_motifs": [
{
"sequence": "AGVYMGNLS",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
},
{
"sequence": "SASKEIKSF",
"count": 4,
"incidence": 80.0,
"motif_short": "I",
"motif_long": "Index",
"metadata": null
}
]
},
{
"position": 3,
"low_support": "LS",
"entropy": 0.7219280948873623,
"support": 5,
"distinct_variants_count": 1,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 20.0,
"diversity_motifs": [
{
"sequence": "GVYMGNLSS",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
},
{
"sequence": "ASKEIKSFL",
"count": 4,
"incidence": 80.0,
"motif_short": "I",
"motif_long": "Index",
"metadata": null
}
]
},
{
"position": 4,
"low_support": "LS",
"entropy": 0.7219280948873623,
"support": 5,
"distinct_variants_count": 1,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 20.0,
"diversity_motifs": [
{
"sequence": "VYMGNLSSQ",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
},
{
"sequence": "SKEIKSFLW",
"count": 4,
"incidence": 80.0,
"motif_short": "I",
"motif_long": "Index",
"metadata": null
}
]
},
{
"position": 5,
"low_support": "LS",
"entropy": 0.7219280948873623,
"support": 5,
"distinct_variants_count": 1,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 20.0,
"diversity_motifs": [
{
"sequence": "KEIKSFLWT",
"count": 4,
"incidence": 80.0,
"motif_short": "I",
"motif_long": "Index",
"metadata": null
},
{
"sequence": "YMGNLSSQQ",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
}
]
},
{
"position": 6,
"low_support": "LS",
"entropy": 0.7219280948873623,
"support": 5,
"distinct_variants_count": 1,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 20.0,
"diversity_motifs": [
{
"sequence": "MGNLSSQQL",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
},
{
"sequence": "EIKSFLWTQ",
"count": 4,
"incidence": 80.0,
"motif_short": "I",
"motif_long": "Index",
"metadata": null
}
]
},
{
"position": 7,
"low_support": "LS",
"entropy": 0.7219280948873623,
"support": 5,
"distinct_variants_count": 1,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 20.0,
"diversity_motifs": [
{
"sequence": "IKSFLWTQS",
"count": 4,
"incidence": 80.0,
"motif_short": "I",
"motif_long": "Index",
"metadata": null
},
{
"sequence": "GNLSSQQLD",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
}
]
},
{
"position": 8,
"low_support": "LS",
"entropy": 0.7219280948873623,
"support": 5,
"distinct_variants_count": 1,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 20.0,
"diversity_motifs": [
{
"sequence": "KSFLWTQSL",
"count": 4,
"incidence": 80.0,
"motif_short": "I",
"motif_long": "Index",
"metadata": null
},
{
"sequence": "NLSSQQLDQ",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
}
]
},
{
"position": 9,
"low_support": "LS",
"entropy": 0.7219280948873623,
"support": 5,
"distinct_variants_count": 1,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 20.0,
"diversity_motifs": [
{
"sequence": "SFLWTQSLR",
"count": 4,
"incidence": 80.0,
"motif_short": "I",
"motif_long": "Index",
"metadata": null
},
{
"sequence": "LSSQQLDQR",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
}
]
},
{
"position": 10,
"low_support": "LS",
"entropy": 0.7219280948873623,
"support": 5,
"distinct_variants_count": 1,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 20.0,
"diversity_motifs": [
{
"sequence": "SSQQLDQRR",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
},
{
"sequence": "FLWTQSLRR",
"count": 4,
"incidence": 80.0,
"motif_short": "I",
"motif_long": "Index",
"metadata": null
}
]
},
{
"position": 11,
"low_support": "LS",
"entropy": 0.7219280948873623,
"support": 5,
"distinct_variants_count": 1,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 20.0,
"diversity_motifs": [
{
"sequence": "LWTQSLRRE",
"count": 4,
"incidence": 80.0,
"motif_short": "I",
"motif_long": "Index",
"metadata": null
},
{
"sequence": "SQQLDQRRA",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
}
]
},
{
"position": 12,
"low_support": "LS",
"entropy": 0.7219280948873623,
"support": 5,
"distinct_variants_count": 1,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 20.0,
"diversity_motifs": [
{
"sequence": "QQLDQRRAL",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
},
{
"sequence": "WTQSLRREL",
"count": 4,
"incidence": 80.0,
"motif_short": "I",
"motif_long": "Index",
"metadata": null
}
]
},
{
"position": 13,
"low_support": "LS",
"entropy": 0.7219280948873623,
"support": 5,
"distinct_variants_count": 1,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 20.0,
"diversity_motifs": [
{
"sequence": "TQSLRRELS",
"count": 4,
"incidence": 80.0,
"motif_short": "I",
"motif_long": "Index",
"metadata": null
},
{
"sequence": "QLDQRRALL",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
}
]
},
{
"position": 14,
"low_support": "LS",
"entropy": 1.3709505944546687,
"support": 5,
"distinct_variants_count": 2,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 40.0,
"diversity_motifs": [
{
"sequence": "QSLRRELSG",
"count": 3,
"incidence": 60.000004,
"motif_short": "I",
"motif_long": "Index",
"metadata": null
},
{
"sequence": "LDQRRALLS",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
},
{
"sequence": "QSLRRELSS",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
}
]
},
{
"position": 15,
"low_support": "LS",
"entropy": 1.3709505944546687,
"support": 5,
"distinct_variants_count": 2,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 40.0,
"diversity_motifs": [
{
"sequence": "DQRRALLSM",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
},
{
"sequence": "SLRRELSGY",
"count": 3,
"incidence": 60.000004,
"motif_short": "I",
"motif_long": "Index",
"metadata": null
},
{
"sequence": "SLRRELSSY",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
}
]
},
{
"position": 16,
"low_support": "LS",
"entropy": 1.3709505944546687,
"support": 5,
"distinct_variants_count": 2,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 40.0,
"diversity_motifs": [
{
"sequence": "QRRALLSMI",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
},
{
"sequence": "LRRELSSYC",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
},
{
"sequence": "LRRELSGYC",
"count": 3,
"incidence": 60.000004,
"motif_short": "I",
"motif_long": "Index",
"metadata": null
}
]
},
{
"position": 17,
"low_support": "LS",
"entropy": 1.3709505944546687,
"support": 5,
"distinct_variants_count": 2,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 40.0,
"diversity_motifs": [
{
"sequence": "RRELSGYCS",
"count": 3,
"incidence": 60.000004,
"motif_short": "I",
"motif_long": "Index",
"metadata": null
},
{
"sequence": "RRALLSMIG",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
},
{
"sequence": "RRELSSYCS",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
}
]
},
{
"position": 18,
"low_support": "LS",
"entropy": 1.3709505944546687,
"support": 5,
"distinct_variants_count": 2,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 40.0,
"diversity_motifs": [
{
"sequence": "RELSGYCSN",
"count": 3,
"incidence": 60.000004,
"motif_short": "I",
"motif_long": "Index",
"metadata": null
},
{
"sequence": "RALLSMIGM",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
},
{
"sequence": "RELSSYCSN",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
}
]
},
{
"position": 19,
"low_support": "LS",
"entropy": 1.3709505944546687,
"support": 5,
"distinct_variants_count": 2,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 40.0,
"diversity_motifs": [
{
"sequence": "ALLSMIGMS",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
},
{
"sequence": "ELSSYCSNI",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
},
{
"sequence": "ELSGYCSNI",
"count": 3,
"incidence": 60.000004,
"motif_short": "I",
"motif_long": "Index",
"metadata": null
}
]
},
{
"position": 20,
"low_support": "LS",
"entropy": 1.3709505944546687,
"support": 5,
"distinct_variants_count": 2,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 40.0,
"diversity_motifs": [
{
"sequence": "LSGYCSNIK",
"count": 3,
"incidence": 60.000004,
"motif_short": "I",
"motif_long": "Index",
"metadata": null
},
{
"sequence": "LLSMIGMSG",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
},
{
"sequence": "LSSYCSNIK",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": null
}
]
}
]
}
dima-cli -i aligned_sequences.afa -o results.json -f "accession|strain|country|date"
from dima import Dima
results = Dima(sequences="aligned_sequences.afa", header_format="accession|strain|country|date").run()
{
"sequence_count": 5,
"support_threshold": 30,
"low_support_count": 20,
"query_name": "Unknown Query",
"kmer_length": 9,
"average_entropy": 0.06854034285524647,
"highest_entropy": {
"position": 186,
"entropy": 1.3921472236645345
},
"results": [
{
"position": 1,
"low_support": "LS",
"entropy": 0.7219280948873623,
"support": 5,
"distinct_variants_count": 1,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 20.0,
"diversity_motifs": [
{
"sequence": "MSASKEIKS",
"count": 4,
"incidence": 80.0,
"motif_short": "I",
"motif_long": "Index",
"metadata": {
"Accession": {
"AYD75365.1": 1,
"QEP52131.1": 1,
"AYD75321.1": 1,
"AYD75325.1": 1
},
"Country": {
"Sierra Leone": 4
},
"Species": {
"Homo sapiens": 3,
"Unknown": 1
},
"Year": {
"1977": 1,
"2012": 1,
"1980": 1,
"1979": 1
}
}
},
{
"sequence": "SAGVYMGNL",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Accession": {
"AYD75329.1": 1
},
"Country": {
"Sierra Leone": 1
},
"Year": {
"1975": 1
},
"Species": {
"Homo sapiens": 1
}
}
}
]
},
{
"position": 2,
"low_support": "LS",
"entropy": 0.7219280948873623,
"support": 5,
"distinct_variants_count": 1,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 20.0,
"diversity_motifs": [
{
"sequence": "SASKEIKSF",
"count": 4,
"incidence": 80.0,
"motif_short": "I",
"motif_long": "Index",
"metadata": {
"Species": {
"Homo sapiens": 3,
"Unknown": 1
},
"Year": {
"1977": 1,
"1980": 1,
"1979": 1,
"2012": 1
},
"Country": {
"Sierra Leone": 4
},
"Accession": {
"AYD75325.1": 1,
"QEP52131.1": 1,
"AYD75365.1": 1,
"AYD75321.1": 1
}
}
},
{
"sequence": "AGVYMGNLS",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Species": {
"Homo sapiens": 1
},
"Year": {
"1975": 1
},
"Accession": {
"AYD75329.1": 1
},
"Country": {
"Sierra Leone": 1
}
}
}
]
},
{
"position": 3,
"low_support": "LS",
"entropy": 0.7219280948873623,
"support": 5,
"distinct_variants_count": 1,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 20.0,
"diversity_motifs": [
{
"sequence": "ASKEIKSFL",
"count": 4,
"incidence": 80.0,
"motif_short": "I",
"motif_long": "Index",
"metadata": {
"Year": {
"1980": 1,
"1977": 1,
"1979": 1,
"2012": 1
},
"Accession": {
"AYD75321.1": 1,
"AYD75365.1": 1,
"QEP52131.1": 1,
"AYD75325.1": 1
},
"Country": {
"Sierra Leone": 4
},
"Species": {
"Unknown": 1,
"Homo sapiens": 3
}
}
},
{
"sequence": "GVYMGNLSS",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Accession": {
"AYD75329.1": 1
},
"Species": {
"Homo sapiens": 1
},
"Country": {
"Sierra Leone": 1
},
"Year": {
"1975": 1
}
}
}
]
},
{
"position": 4,
"low_support": "LS",
"entropy": 0.7219280948873623,
"support": 5,
"distinct_variants_count": 1,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 20.0,
"diversity_motifs": [
{
"sequence": "SKEIKSFLW",
"count": 4,
"incidence": 80.0,
"motif_short": "I",
"motif_long": "Index",
"metadata": {
"Accession": {
"AYD75325.1": 1,
"AYD75365.1": 1,
"QEP52131.1": 1,
"AYD75321.1": 1
},
"Country": {
"Sierra Leone": 4
},
"Species": {
"Unknown": 1,
"Homo sapiens": 3
},
"Year": {
"2012": 1,
"1979": 1,
"1980": 1,
"1977": 1
}
}
},
{
"sequence": "VYMGNLSSQ",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Accession": {
"AYD75329.1": 1
},
"Year": {
"1975": 1
},
"Species": {
"Homo sapiens": 1
},
"Country": {
"Sierra Leone": 1
}
}
}
]
},
{
"position": 5,
"low_support": "LS",
"entropy": 0.7219280948873623,
"support": 5,
"distinct_variants_count": 1,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 20.0,
"diversity_motifs": [
{
"sequence": "KEIKSFLWT",
"count": 4,
"incidence": 80.0,
"motif_short": "I",
"motif_long": "Index",
"metadata": {
"Accession": {
"QEP52131.1": 1,
"AYD75325.1": 1,
"AYD75321.1": 1,
"AYD75365.1": 1
},
"Year": {
"1979": 1,
"1980": 1,
"1977": 1,
"2012": 1
},
"Country": {
"Sierra Leone": 4
},
"Species": {
"Homo sapiens": 3,
"Unknown": 1
}
}
},
{
"sequence": "YMGNLSSQQ",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Country": {
"Sierra Leone": 1
},
"Year": {
"1975": 1
},
"Species": {
"Homo sapiens": 1
},
"Accession": {
"AYD75329.1": 1
}
}
}
]
},
{
"position": 6,
"low_support": "LS",
"entropy": 0.7219280948873623,
"support": 5,
"distinct_variants_count": 1,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 20.0,
"diversity_motifs": [
{
"sequence": "MGNLSSQQL",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Accession": {
"AYD75329.1": 1
},
"Country": {
"Sierra Leone": 1
},
"Species": {
"Homo sapiens": 1
},
"Year": {
"1975": 1
}
}
},
{
"sequence": "EIKSFLWTQ",
"count": 4,
"incidence": 80.0,
"motif_short": "I",
"motif_long": "Index",
"metadata": {
"Accession": {
"AYD75321.1": 1,
"QEP52131.1": 1,
"AYD75365.1": 1,
"AYD75325.1": 1
},
"Species": {
"Unknown": 1,
"Homo sapiens": 3
},
"Country": {
"Sierra Leone": 4
},
"Year": {
"1977": 1,
"1980": 1,
"2012": 1,
"1979": 1
}
}
}
]
},
{
"position": 7,
"low_support": "LS",
"entropy": 0.7219280948873623,
"support": 5,
"distinct_variants_count": 1,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 20.0,
"diversity_motifs": [
{
"sequence": "GNLSSQQLD",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Country": {
"Sierra Leone": 1
},
"Species": {
"Homo sapiens": 1
},
"Accession": {
"AYD75329.1": 1
},
"Year": {
"1975": 1
}
}
},
{
"sequence": "IKSFLWTQS",
"count": 4,
"incidence": 80.0,
"motif_short": "I",
"motif_long": "Index",
"metadata": {
"Accession": {
"AYD75365.1": 1,
"AYD75325.1": 1,
"QEP52131.1": 1,
"AYD75321.1": 1
},
"Year": {
"1979": 1,
"1980": 1,
"1977": 1,
"2012": 1
},
"Species": {
"Unknown": 1,
"Homo sapiens": 3
},
"Country": {
"Sierra Leone": 4
}
}
}
]
},
{
"position": 8,
"low_support": "LS",
"entropy": 0.7219280948873623,
"support": 5,
"distinct_variants_count": 1,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 20.0,
"diversity_motifs": [
{
"sequence": "NLSSQQLDQ",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Country": {
"Sierra Leone": 1
},
"Year": {
"1975": 1
},
"Species": {
"Homo sapiens": 1
},
"Accession": {
"AYD75329.1": 1
}
}
},
{
"sequence": "KSFLWTQSL",
"count": 4,
"incidence": 80.0,
"motif_short": "I",
"motif_long": "Index",
"metadata": {
"Country": {
"Sierra Leone": 4
},
"Year": {
"1979": 1,
"2012": 1,
"1977": 1,
"1980": 1
},
"Species": {
"Unknown": 1,
"Homo sapiens": 3
},
"Accession": {
"AYD75325.1": 1,
"AYD75365.1": 1,
"AYD75321.1": 1,
"QEP52131.1": 1
}
}
}
]
},
{
"position": 9,
"low_support": "LS",
"entropy": 0.7219280948873623,
"support": 5,
"distinct_variants_count": 1,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 20.0,
"diversity_motifs": [
{
"sequence": "SFLWTQSLR",
"count": 4,
"incidence": 80.0,
"motif_short": "I",
"motif_long": "Index",
"metadata": {
"Year": {
"2012": 1,
"1979": 1,
"1980": 1,
"1977": 1
},
"Accession": {
"QEP52131.1": 1,
"AYD75325.1": 1,
"AYD75365.1": 1,
"AYD75321.1": 1
},
"Country": {
"Sierra Leone": 4
},
"Species": {
"Unknown": 1,
"Homo sapiens": 3
}
}
},
{
"sequence": "LSSQQLDQR",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Species": {
"Homo sapiens": 1
},
"Accession": {
"AYD75329.1": 1
},
"Year": {
"1975": 1
},
"Country": {
"Sierra Leone": 1
}
}
}
]
},
{
"position": 10,
"low_support": "LS",
"entropy": 0.7219280948873623,
"support": 5,
"distinct_variants_count": 1,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 20.0,
"diversity_motifs": [
{
"sequence": "FLWTQSLRR",
"count": 4,
"incidence": 80.0,
"motif_short": "I",
"motif_long": "Index",
"metadata": {
"Year": {
"1977": 1,
"2012": 1,
"1980": 1,
"1979": 1
},
"Accession": {
"AYD75321.1": 1,
"AYD75325.1": 1,
"AYD75365.1": 1,
"QEP52131.1": 1
},
"Species": {
"Unknown": 1,
"Homo sapiens": 3
},
"Country": {
"Sierra Leone": 4
}
}
},
{
"sequence": "SSQQLDQRR",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Species": {
"Homo sapiens": 1
},
"Year": {
"1975": 1
},
"Accession": {
"AYD75329.1": 1
},
"Country": {
"Sierra Leone": 1
}
}
}
]
},
{
"position": 11,
"low_support": "LS",
"entropy": 0.7219280948873623,
"support": 5,
"distinct_variants_count": 1,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 20.0,
"diversity_motifs": [
{
"sequence": "LWTQSLRRE",
"count": 4,
"incidence": 80.0,
"motif_short": "I",
"motif_long": "Index",
"metadata": {
"Country": {
"Sierra Leone": 4
},
"Accession": {
"QEP52131.1": 1,
"AYD75365.1": 1,
"AYD75325.1": 1,
"AYD75321.1": 1
},
"Species": {
"Homo sapiens": 3,
"Unknown": 1
},
"Year": {
"1979": 1,
"1980": 1,
"2012": 1,
"1977": 1
}
}
},
{
"sequence": "SQQLDQRRA",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Accession": {
"AYD75329.1": 1
},
"Species": {
"Homo sapiens": 1
},
"Country": {
"Sierra Leone": 1
},
"Year": {
"1975": 1
}
}
}
]
},
{
"position": 12,
"low_support": "LS",
"entropy": 0.7219280948873623,
"support": 5,
"distinct_variants_count": 1,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 20.0,
"diversity_motifs": [
{
"sequence": "QQLDQRRAL",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Country": {
"Sierra Leone": 1
},
"Species": {
"Homo sapiens": 1
},
"Year": {
"1975": 1
},
"Accession": {
"AYD75329.1": 1
}
}
},
{
"sequence": "WTQSLRREL",
"count": 4,
"incidence": 80.0,
"motif_short": "I",
"motif_long": "Index",
"metadata": {
"Country": {
"Sierra Leone": 4
},
"Year": {
"1980": 1,
"2012": 1,
"1979": 1,
"1977": 1
},
"Accession": {
"QEP52131.1": 1,
"AYD75321.1": 1,
"AYD75325.1": 1,
"AYD75365.1": 1
},
"Species": {
"Homo sapiens": 3,
"Unknown": 1
}
}
}
]
},
{
"position": 13,
"low_support": "LS",
"entropy": 0.7219280948873623,
"support": 5,
"distinct_variants_count": 1,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 20.0,
"diversity_motifs": [
{
"sequence": "TQSLRRELS",
"count": 4,
"incidence": 80.0,
"motif_short": "I",
"motif_long": "Index",
"metadata": {
"Accession": {
"AYD75365.1": 1,
"AYD75321.1": 1,
"QEP52131.1": 1,
"AYD75325.1": 1
},
"Country": {
"Sierra Leone": 4
},
"Year": {
"1977": 1,
"1979": 1,
"2012": 1,
"1980": 1
},
"Species": {
"Unknown": 1,
"Homo sapiens": 3
}
}
},
{
"sequence": "QLDQRRALL",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Year": {
"1975": 1
},
"Accession": {
"AYD75329.1": 1
},
"Country": {
"Sierra Leone": 1
},
"Species": {
"Homo sapiens": 1
}
}
}
]
},
{
"position": 14,
"low_support": "LS",
"entropy": 1.3709505944546687,
"support": 5,
"distinct_variants_count": 2,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 40.0,
"diversity_motifs": [
{
"sequence": "QSLRRELSG",
"count": 3,
"incidence": 60.000004,
"motif_short": "I",
"motif_long": "Index",
"metadata": {
"Country": {
"Sierra Leone": 3
},
"Accession": {
"AYD75325.1": 1,
"AYD75321.1": 1,
"AYD75365.1": 1
},
"Species": {
"Homo sapiens": 2,
"Unknown": 1
},
"Year": {
"1979": 1,
"1980": 1,
"1977": 1
}
}
},
{
"sequence": "QSLRRELSS",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Country": {
"Sierra Leone": 1
},
"Year": {
"2012": 1
},
"Species": {
"Homo sapiens": 1
},
"Accession": {
"QEP52131.1": 1
}
}
},
{
"sequence": "LDQRRALLS",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Country": {
"Sierra Leone": 1
},
"Species": {
"Homo sapiens": 1
},
"Accession": {
"AYD75329.1": 1
},
"Year": {
"1975": 1
}
}
}
]
},
{
"position": 15,
"low_support": "LS",
"entropy": 1.3709505944546687,
"support": 5,
"distinct_variants_count": 2,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 40.0,
"diversity_motifs": [
{
"sequence": "DQRRALLSM",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Country": {
"Sierra Leone": 1
},
"Accession": {
"AYD75329.1": 1
},
"Species": {
"Homo sapiens": 1
},
"Year": {
"1975": 1
}
}
},
{
"sequence": "SLRRELSSY",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Accession": {
"QEP52131.1": 1
},
"Country": {
"Sierra Leone": 1
},
"Species": {
"Homo sapiens": 1
},
"Year": {
"2012": 1
}
}
},
{
"sequence": "SLRRELSGY",
"count": 3,
"incidence": 60.000004,
"motif_short": "I",
"motif_long": "Index",
"metadata": {
"Species": {
"Unknown": 1,
"Homo sapiens": 2
},
"Year": {
"1977": 1,
"1980": 1,
"1979": 1
},
"Country": {
"Sierra Leone": 3
},
"Accession": {
"AYD75365.1": 1,
"AYD75325.1": 1,
"AYD75321.1": 1
}
}
}
]
},
{
"position": 16,
"low_support": "LS",
"entropy": 1.3709505944546687,
"support": 5,
"distinct_variants_count": 2,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 40.0,
"diversity_motifs": [
{
"sequence": "LRRELSSYC",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Country": {
"Sierra Leone": 1
},
"Accession": {
"QEP52131.1": 1
},
"Year": {
"2012": 1
},
"Species": {
"Homo sapiens": 1
}
}
},
{
"sequence": "LRRELSGYC",
"count": 3,
"incidence": 60.000004,
"motif_short": "I",
"motif_long": "Index",
"metadata": {
"Year": {
"1979": 1,
"1977": 1,
"1980": 1
},
"Species": {
"Unknown": 1,
"Homo sapiens": 2
},
"Country": {
"Sierra Leone": 3
},
"Accession": {
"AYD75365.1": 1,
"AYD75321.1": 1,
"AYD75325.1": 1
}
}
},
{
"sequence": "QRRALLSMI",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Species": {
"Homo sapiens": 1
},
"Country": {
"Sierra Leone": 1
},
"Accession": {
"AYD75329.1": 1
},
"Year": {
"1975": 1
}
}
}
]
},
{
"position": 17,
"low_support": "LS",
"entropy": 1.3709505944546687,
"support": 5,
"distinct_variants_count": 2,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 40.0,
"diversity_motifs": [
{
"sequence": "RRELSSYCS",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Year": {
"2012": 1
},
"Accession": {
"QEP52131.1": 1
},
"Country": {
"Sierra Leone": 1
},
"Species": {
"Homo sapiens": 1
}
}
},
{
"sequence": "RRELSGYCS",
"count": 3,
"incidence": 60.000004,
"motif_short": "I",
"motif_long": "Index",
"metadata": {
"Species": {
"Homo sapiens": 2,
"Unknown": 1
},
"Year": {
"1980": 1,
"1977": 1,
"1979": 1
},
"Accession": {
"AYD75325.1": 1,
"AYD75365.1": 1,
"AYD75321.1": 1
},
"Country": {
"Sierra Leone": 3
}
}
},
{
"sequence": "RRALLSMIG",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Country": {
"Sierra Leone": 1
},
"Species": {
"Homo sapiens": 1
},
"Accession": {
"AYD75329.1": 1
},
"Year": {
"1975": 1
}
}
}
]
},
{
"position": 18,
"low_support": "LS",
"entropy": 1.3709505944546687,
"support": 5,
"distinct_variants_count": 2,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 40.0,
"diversity_motifs": [
{
"sequence": "RALLSMIGM",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Year": {
"1975": 1
},
"Accession": {
"AYD75329.1": 1
},
"Country": {
"Sierra Leone": 1
},
"Species": {
"Homo sapiens": 1
}
}
},
{
"sequence": "RELSSYCSN",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Species": {
"Homo sapiens": 1
},
"Accession": {
"QEP52131.1": 1
},
"Country": {
"Sierra Leone": 1
},
"Year": {
"2012": 1
}
}
},
{
"sequence": "RELSGYCSN",
"count": 3,
"incidence": 60.000004,
"motif_short": "I",
"motif_long": "Index",
"metadata": {
"Accession": {
"AYD75325.1": 1,
"AYD75365.1": 1,
"AYD75321.1": 1
},
"Species": {
"Homo sapiens": 2,
"Unknown": 1
},
"Year": {
"1980": 1,
"1977": 1,
"1979": 1
},
"Country": {
"Sierra Leone": 3
}
}
}
]
},
{
"position": 19,
"low_support": "LS",
"entropy": 1.3709505944546687,
"support": 5,
"distinct_variants_count": 2,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 40.0,
"diversity_motifs": [
{
"sequence": "ELSGYCSNI",
"count": 3,
"incidence": 60.000004,
"motif_short": "I",
"motif_long": "Index",
"metadata": {
"Country": {
"Sierra Leone": 3
},
"Species": {
"Homo sapiens": 2,
"Unknown": 1
},
"Accession": {
"AYD75365.1": 1,
"AYD75325.1": 1,
"AYD75321.1": 1
},
"Year": {
"1977": 1,
"1979": 1,
"1980": 1
}
}
},
{
"sequence": "ELSSYCSNI",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Accession": {
"QEP52131.1": 1
},
"Species": {
"Homo sapiens": 1
},
"Country": {
"Sierra Leone": 1
},
"Year": {
"2012": 1
}
}
},
{
"sequence": "ALLSMIGMS",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Country": {
"Sierra Leone": 1
},
"Accession": {
"AYD75329.1": 1
},
"Species": {
"Homo sapiens": 1
},
"Year": {
"1975": 1
}
}
}
]
},
{
"position": 20,
"low_support": "LS",
"entropy": 1.3709505944546687,
"support": 5,
"distinct_variants_count": 2,
"distinct_variants_incidence": 100.0,
"total_variants_incidence": 40.0,
"diversity_motifs": [
{
"sequence": "LLSMIGMSG",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Accession": {
"AYD75329.1": 1
},
"Country": {
"Sierra Leone": 1
},
"Species": {
"Homo sapiens": 1
},
"Year": {
"1975": 1
}
}
},
{
"sequence": "LSGYCSNIK",
"count": 3,
"incidence": 60.000004,
"motif_short": "I",
"motif_long": "Index",
"metadata": {
"Country": {
"Sierra Leone": 3
},
"Year": {
"1979": 1,
"1977": 1,
"1980": 1
},
"Accession": {
"AYD75365.1": 1,
"AYD75321.1": 1,
"AYD75325.1": 1
},
"Species": {
"Unknown": 1,
"Homo sapiens": 2
}
}
},
{
"sequence": "LSSYCSNIK",
"count": 1,
"incidence": 20.0,
"motif_short": "U",
"motif_long": "Unique",
"metadata": {
"Year": {
"2012": 1
},
"Species": {
"Homo sapiens": 1
},
"Accession": {
"QEP52131.1": 1
},
"Country": {
"Sierra Leone": 1
}
}
}
]
}
]
}
| Argument | Type | Required | Default | Example | Description |
|---|---|---|---|---|---|
| -h | N/A | False | N/A | dima-cli -h | Prints a summary of all available command-line arguments. |
| -n | String | False | Unknown | dima-cli -i sequences.afa -o results.json -f "accession|strain|country" -n "NA" -n "Unknown" | Silently fix missing values in the FASTA header with given value. |
| -v | N/A | False | N/A | dima-cli -v | Prints the version of dima-cli that is currently installed. |
| -q | String | False | Unknown Query | dima-cli -q "Coronavirus Surface Protein" -i sequences.afa -o results.json | The name of the sample that will appear on the results. |
| -i | String | True | N/A | dima-cli -i sequences.afa -o results.json | The path to the FASTA Multiple Sequence Alignment file. |
| -o | String | True | N/A | dima-cli -i sequences.afa -o results,json | The location where the results shall be saved. |
| -l | Integer | False | 9 | dima-cli -i sequences.afa -l 12 -o results.json | The length of the kmers generated. |
| -f | String | False | N/A | dima-cli -i sequences.afa -f "accession|strain|country" -o results.json | The format of the FASTA header. Labels where each variant of a kmer position originated from. |
| -s | Integer | False | 30 | dima-cli -i sequences.afa -l 12 -s 40 -o results.json | The minimum required support for each kmer position. |
| -a | nucleotide/protein | False | protein | dima-cli -i dna_sequences.afa -a nucleotide -o results.json | The alphabet of the sequences (ie: protein/nucleotide, default: protein) |
| -t | json/xlsx | False | json | dima-cli -i dna_sequences.afa -a nucleotide -o results.json -t xlsx | The output format (ie: json/xlsx, default: json) |
| -c | String | False | N/A | dima-cli -i dna_sequences.afa -a nucleotide -o results.json -c hcs.json | Path to save Highly Conserved Sequences (HCS) in JSON format. |
| -e | Float | False | 100 | dima-cli -i dna_sequences.afa -a nucleotide -o results.json -c hcs.json -e 90.5 | Minimum incidence (%) threshold for HCS concatenation. |
| Parameter | Type | Required | Default | Description |
|---|---|---|---|---|
| sequences | String/StringIO | True | N/A | The path to a FASTA Multiple Sequence Alignment file (MSA), or a StringIO object containing FASTA MSA. |
| kmer_length | Integer | False | 9 | The length of the kmers generated. |
| header_fillna | String | False | Unknown | Silently fix missing values in the FASTA header with given value (only required when header_format is given). |
| header_format | String | False | N/A | The format of the FASTA header. Labels where each variant of a kmer position originated from. |
| support_threshold | Integer | False | 30 | The minimum required support for each kmer position. |
| query_name | String | False | Unknown Query | The name of the sample that will appear on the results. |
| alphabet | String | False | protein | The alphabet of the sequences (ie: protein/nucleotide, default: protein) |
FAQs
A command-line tool that analyses the diversity and motifs of biological sequences
We found that dima-cli demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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The Socket Research Team breaks down a malicious wrapper package that uses obfuscation to harvest credentials and exfiltrate sensitive data.
Research
Security News
Attackers used a malicious npm package typosquatting a popular ESLint plugin to steal sensitive data, execute commands, and exploit developer systems.
Security News
The Ultralytics' PyPI Package was compromised four times in one weekend through GitHub Actions cache poisoning and failure to rotate previously compromised API tokens.