0001846: Issue with building tree for proteins containing selenocysteine residues - MantisBT

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ID

Project

Category

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Date Submitted

Last Update

0001846

MEGA

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public

2020-03-15 17:14

2020-03-23 13:33

Reporter

guest

Assigned To

gstecher

Priority

normal

Severity

minor

Reproducibility

have not tried

Status

resolved

Resolution

won't fix

Platform

PC

OS

Linux

Product Version

MEGA-CC 11 (command line version)

Target Version

Fixed in Version

Summary

0001846: Issue with building tree for proteins containing selenocysteine residues

Description

Hi MEGA team,

I am using MEGAX to building a phylogenetic tree for the protein arsenate reductase, some of which contain the unusual amino acid selenocysteine (symbol U). MEGAX seems to be unable to recognize selenocysteine residues and fails to build the tree. The error is as follows: Error: Unable to read your file, error at line 22354 details: Invalid Amino found. Expecting an amino acid, but found 'U'.

Is there any way MEGAX be able to work on these proteins?

Thanks,
Bob

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First Name

Pok Man

Last Name

Leung

Email

pok.leung@monash.edu

Confirm Email

pok.leung@monash.edu

Relationships

Notes
(0004432) gstecher (administrator) 2020-03-23 13:33	Hi Pok Man, I am writing in response to your question regarding the MEGA software. Unfortunately the models implemented in MEGA do not support selenocysteine. However, you could replace all the U bases in your data with a ? character in which case they would be treated as missing data. -- Best regards, Glen Stecher Institute for Genomics and Evolutionary Medicine igem.temple.edu

Issue History
Date Modified	Username	Field	Change
1969-12-31 17:33	user19	Status	new => assigned
1969-12-31 17:33	user19	Assigned To	=> agasky
1969-12-31 17:33	agasky	Status	assigned => closed
1969-12-31 17:33	agasky	Resolution	open => fixed
2020-03-15 17:14	guest	New Issue
2020-03-23 13:33	gstecher	Note Added: 0004432
2020-03-23 13:33	gstecher	Status	new => resolved
2020-03-23 13:33	gstecher	Resolution	open => won't fix
2020-03-23 13:33	gstecher	Assigned To	=> gstecher

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