A new open-source tool that integrates pipeline automated identification and phylogenetic studies of microbial communities using genes sequences

Tutorial

A. Install and Use

Deploy BacSearch in a Java Web Server (like Apache Tomcat). After the deployment, remove the .war file from the webapps folder (if the file is still there) and follow the instructions in the own configuration file (rnas.properties) of the application. Finished, start the server, open your browser and it will be ready to be used with Genbank accessing the address http://server:port/bacsearch, generally http://localhost:8080/bacsearch.

B. System Requirements

1.Java (compulsory):

BacSearch needs a recent version of Java (Recommended Version 6 Update 26 ).

http://www.java.com/en/download/manual.jsp

2.Flow of installation and configuration:

3.Databases (optional - for local use):

  Name Size
RDP-II - 10.26 Archae
Large
RDP-II - 10.26 Bacteria
Large
RDP-II - 10.26 Archae and Bacteria
Large
RDP-II - 10.26 Genbank Combined
Large
FUNGENE - fusA DNA FASTA
Small
FUNGENE - ileS DNA FASTA
Small
FUNGENE - lepA DNA FASTA
Small
FUNGENE - leuS DNA FASTA
Small
FUNGENE - pyrG DNA FASTA
Small
FUNGENE - recA DNA FASTA
Small
FUNGENE - recG DNA FASTA
Small
FUNGENE - rp1B DNA FASTA
Small
FUNGENE - rpoB DNA FASTA
Small
Greengenes ARB Database ARB 16S
233MB
Greengenes Fasta data files: Fasta data files
Varied
Greengenes Format: greengenes16SrRNAgenes.txt.gz
945M
SILVA SSU SSU - REF
285MB
SILVA SSU HSM/MVM
194MB
SILVA SSU REF NR
226MB
SILVA SSU PARC
992MB
SILVA LSU REF
45MB
SILVA LSU PARC
107MB

C. Usage

©2011 BacSearch: Web Server

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  • Cidade Universitária, Campus I.
  • Laboratório de Tecnologia Farmacêutica
  • Joao Pessoa - PB
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