AMnrGC - Amazon river non-reduntant microbial genes catalogue
- 1. Federal University of São Carlos, São Carlos / SP - Brazil
- 2. Institut del Ciencias del Mar, Barcelona - Spain
Description
AMnrGC : Amazon river basin non-redundant microbial gene catalogue
RELEASE 2018/01
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1. INTRODUCTION
AMnrGC is a collection of genes and proteins which were constructed
by use of Amazon river basin openly available metagenomes from
sequencing projects (SRP044326, PRJEB25171 and SRP039390). Briefly,
metagenomes were coassembled by groups made up their geographical
location with Megahit v.1.0 and the contigs were used to gene predictions
by Prodigal v.2.6.3. Genes sequences were length filtered (> 150 bp) and
clustered by CD-HIT-EST (version 4.6) at 95% of nucleotide identity and
90% of overlap of the shorter gene. Theorical protein products were annotated
by the most completes databases up to date and their complete information
is available here.
2. LOCATION
AMnrGC versions will be available on the web only under the current ZENODO
repository: 10.5281/zenodo.1484504
3. FORMAT
Gene entries were named as ">AM_AGSSY_XXX" where XXX represents an unique numerical
identifier. Genes were deposited in their coding phase, because of this, all of them
can be used to generate the protein sequences by transeq function at ORF+1.
The protein entries correspond to genes artifical translation used in the annotations,
and also available, codified in the same way, but containing the indication "_1" in
the end of the header. Example:
Gene:
>AM_AGSSY_151515
Protein:
>AM_AGSSY_151515_1
Annotations were provided as separate tables for each database used to annotate the
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.
New versions should include updated versions of annotations or even additional sequences,
numbered as subsequent entries.
3. ACKNOWLEDGEMENTS
This work is a joint effort of Laboratory of molecular biology from Federal
University of São Carlos, São Paulo, Brazil (LBM/UFSCAR) and Protists group
of Institut del Ciencias del Mar, Barcelone, Spain (ICM). We are grateful to
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
the AMnrGC consortium.
Current curators:
- Célio Dias Santos Júnior (celio.diasjunior@gmail.com)
- Flavio Henrique-Silva (dfhs@ufscar.br)
- Ramiro R. Logares (ramiro.logares@icm.csic.es)
5. COPYRIGHT NOTICE
AMnrGC - Amazon river basin non-redundant microbial gene catalogue
Copyright (C) 2018 The AMnrGC consortium.
This database is provided “as is” and without any warranty of any kind,
of openly available for non-commerical purposes. You can redistribute and/or modify it
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
2018
Files
README_AMnrGC_v.2018-01.txt
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Additional details
References
- Santos-Júnior, 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