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PGAB: From genome sequence to draft model

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PGAB: PGAP based pipeline

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Note

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This pipeline is still in the idea stage and will be object to a future update.

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Generating a model for an organism where no information on genes and proteins is obtainable via any database +causes the problem that the model will not contain valid database identifiers for any GeneProduct. To resolve this issue the +workflow in Figure Fig. 1 can be used.

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  1. First annotate the genome with NCBI’s Prokaryotic Genome Annotation Pipeline (PGAP) to obtain the same FASTA format as used in NCBI and use the flag for taxonomy checking.

    2. +

  2. Then use DIAMOND with the nr database from NCBI and the obtained annotated FASTA file as input. Restrict the search to your organism’s taxon if known.

    3. +

  3. Check if any protein in the annotation FASTA file still has no database identifier.

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    -> YES: Rerun DIAMOND without the taxonomy check and without the restriction for the organism’s taxon.
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    -> NO: Continue with step 4.
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    4. +

  4. Add the DIAMOND result to the annotated FASTA file.

    5. +

  5. Run e.g. CarveMe to obtain a draft model.

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  6. Check if in the model any GeneProducts without NCBI Protein or RefSeq identifiers occur.

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    -> YES:
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    i. Use individual BLAST searches for the remaining GeneProducts.
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    ii. Add the results to the annotated and refined FASTA file.
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    iii. Create again a draft model with the same program with the newly refined FASTA file.
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    -> NO: The draft model is done.
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    7. +
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+Workflow from genome sequence to a draft model
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Fig. 1 Workflow from genome sequence to a draft model

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