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Merge pull request tseemann#513 from smsaladi/patch-1
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fix typos in README.md
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tseemann authored Aug 4, 2020
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[![DOI:10.1093/bioinformatics/btu153](https://zenodo.org/badge/DOI/10.1093/bioinformatics/btu153.svg)](https://doi.org/10.1093/bioinformatics/btu153)
![Don't judge me](https://img.shields.io/badge/Language-Perl_5-steelblue.svg)

# Prokka: rapid prokaryotic genome annotation
# Prokka: rapid prokaryotic genome annotation

## Introduction

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### Option: --rawproduct

Prokka annotates proteins by using sequence similarity to other proteins in its database,
or the databses the user provides via `--proteins`. By default, Prokka tries to "cleans" the
or the databases the user provides via `--proteins`. By default, Prokka tries to "cleans" the
`/product` names to ensure they are compliant with Genbank/ENA conventions.
Some of the main things it does is:

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### The Core (BLAST+) Databases

Prokka uses a variety of databases when trying to assign function to the
predicted CDS features. It takes a hierarchial approach to make it fast.
predicted CDS features. It takes a hierarchical approach to make it fast.
A small, core set of well characterized proteins are first searched using
BLAST+. This combination of small database and fast search typically
completes about 70% of the workload. Then a series of slower but more
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can't handle multi-exon gene models; I would recommend using MAKER 2 for
that purpose.

* __Why does Prokka keeps on crashing when it gets to tge "tbl2asn" stage?__
* __Why does Prokka keeps on crashing when it gets to the "tbl2asn" stage?__
It seems that the tbl2asn program from NCBI "expires" after 6-12 months, and
refuses to run. Unfortunately you need to install a newer version which you
can download from [here](http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/).
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