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.
Did you know?
Socket for GitHub automatically highlights issues in each pull request and monitors the health of all your open source dependencies. Discover the contents of your packages and block harmful activity before you install or update your dependencies.
Security News
Experts push back on new claims about AI-driven ransomware, warning that hype and sponsored research are distorting how the threat is understood.
Security News
Ruby's creator Matz assumes control of RubyGems and Bundler repositories while former maintainers agree to step back and transfer all rights to end the dispute.
Research
/Security News
Socket researchers found 10 typosquatted npm packages that auto-run on install, show fake CAPTCHAs, fingerprint by IP, and deploy a credential stealer.