DiMA - Diversity Motif Analyser

Table of Contents

• What is DiMA?
• Publications
• Installation
• Basic Usage
  • Shell Command
  • Python
  • Results
• Advance Usage
  • Shell Command
  • Python
  • Results
• Command-Line Arguments
• Module Parameters

What is DiMA?

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.

• Index: The predominant sequence.
• Major: The sequence with the second highest incidence after the Index.
• Minor: Kmers with incidence in between major and unique motifs
• Unique: Kmers which are only seen once in a particular kmer position.

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.

Publications

• https://arxiv.org/abs/2205.13915

Installation

pip install dima-cli

Basic Usage

Shell Command

dima-cli -i aligned_sequences.afa -o results.json

Python

from dima import Dima
results = Dima(sequences="aligned_sequences.afa").run()

Results

<details> <summary>Click to view basic results</summary>

{
  "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",