DOI: 10.5281/zenodo.1484504
title: AMnrGC - Amazon river non-reduntant microbial genes catalogue

description: <strong>AMnrGC : Amazon river basin non-redundant microbial gene catalogue</strong>

 

                        RELEASE 2018/01<br>
                    --------------------------------------

 

1. INTRODUCTION

   AMnrGC is a collection of genes and proteins which were constructed<br>
   by use of Amazon river basin openly available metagenomes from<br>
   sequencing projects (SRP044326, PRJEB25171 and SRP039390). Briefly,<br>
   metagenomes were coassembled by groups made up their geographical<br>
   location with Megahit v.1.0 and the contigs were used to gene predictions<br>
   by Prodigal v.2.6.3. Genes sequences were length filtered (&gt; 150 bp) and<br>
   clustered by CD-HIT-EST (version 4.6) at 95% of nucleotide identity and<br>
   90% of overlap of the shorter gene. Theorical protein products were annotated<br>
   by the most completes databases up to date and their complete information<br>
   is available here.

 

2. LOCATION

   AMnrGC versions will be available on the web only under the current ZENODO<br>
   repository: 10.5281/zenodo.1484504

 

3. FORMAT

   Gene entries were named as "&gt;AM_AGSSY_XXX" where XXX represents an unique numerical<br>
   identifier. Genes were deposited in their coding phase, because of this, all of them<br>
   can be used to generate the protein sequences by transeq function at ORF+1.<br>
   The protein entries correspond to genes artifical translation used in the annotations,<br>
   and also available, codified in the same way, but containing the indication "_1" in<br>
   the end of the header. Example:

    Gene:<br>
    &gt;AM_AGSSY_151515

    Protein:<br>
    &gt;AM_AGSSY_151515_1

   Annotations were provided as separate tables for each database used to annotate the<br>
   sequences. The header of these tables indicates the meaning of each value.

 

2. FUTURE FORMAT CHANGES

   No major changes are expected for the main general format of the database.<br>
   New versions should include updated versions of annotations or even additional sequences,<br>
   numbered as subsequent entries.

 

3. ACKNOWLEDGEMENTS<br>
   <br>
   This work is a joint effort of Laboratory of molecular biology from Federal<br>
   University of São Carlos, São Paulo, Brazil (LBM/UFSCAR) and Protists group<br>
   of Institut del Ciencias del Mar, Barcelone, Spain (ICM). We are grateful to<br>
   Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), as well as,                      the spanish funding organ Consejo Superior de Investigaciones Científicas (CSIC).

 

        This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal                      de Nível Superior - Brasil (CAPES) - Finance Code 001.

 

4. THE AMnrGC TEAM

   AMnrGC is maintained by a group of researchers. You can contact<br>
   the AMnrGC consortium.<br>
   <br>
   Current curators:

   - Célio Dias Santos Júnior (celio.diasjunior@gmail.com)<br>
   - Flavio Henrique-Silva (dfhs@ufscar.br)<br>
   - Ramiro R. Logares (ramiro.logares@icm.csic.es)<br>
 

5. COPYRIGHT NOTICE

   AMnrGC - Amazon river basin non-redundant microbial gene catalogue<br>
   Copyright (C) 2018 The AMnrGC consortium.

   This database is provided “as is” and without any warranty of any kind,<br>
   of openly available for non-commerical purposes. You can redistribute and/or modify it<br>
   as you wish, under the terms of the ODBL 1.0 license:

    https://opendatacommons.org/licenses/odbl/1.0/

   For commercial purposes, please contact us.  

___________________

The AMnrGC Consortium<br>
2018
description: {"references": ["Santos-J\u00fanior, CD et al. 2019. Uncovering the gene machinery of the Amazon River microbiome to degrade rainforest organic matter. BioRxiv 585562; doi: https://doi.org/10.1101/585562"]}