[maker-devel] (no subject)

[Fields, Christopher J]

If you have a fairly recent version of Bioperl (now at 1.7.1) this should not be an issue within bioperl (note this isn’t a bug per se, just that the default universal codon table has rare codons so we simply added a ‘strict’ alternative table).

Also, based on that thread Carson also added a workaround in MAKER explicitly setting a ‘strict’ codon table that should be in 3.00.

chris

From: maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of Nathan Ricks <nathan.ricks at gmail.com>
Date: Wednesday, August 2, 2017 at 9:54 PM
To: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: [maker-devel] (no subject)

As I have been submitting my genome sequences to NCBI, I've come to realise that about 1/10 of the transcripts generated have an incorrect start codon. When I look at the genes manually, they usually have a start codon 3 or 6 base pairs away. What could be causing this?
I read about a previous issue where there was a mistake in Bioperl and the fix was implemented many version ago. I have maker version 3.00

https://groups.google.com/forum/#!searchin/maker-devel/start$20codon|sort:relevance/maker-devel/S0j1fJ4LjVY/5ugSG01kKkUJ
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