![]() The alignment length shows the user how much of the AR database gene is found on your genome. The user is free to pick a value for X.īelow the potential new variants SSTAR lists the AR genes that share 100% sequence similarity with AR genes in the used database. These are the variants that share between X% and 99.99% sequence similarity with an AR gene in the used database. The contig, scaffold or chromosome where the AR gene is locatedįirst, SSTAR lists the potential new alleles or variants at the top of the window.Each output line contains five fields, separated by a tab: The second output window displays the AR resistance genes and porins that are identified on your input genome assembly. The genes will be listed in the the second output window. The ‘Identify resistance genes’ button starts the actual AR gene annotation process. A value between 80 and 99% is recommended. One needs to enter a sequence similarity percentage value that serves as cut-off for detecting potential new variants of AR genes. The top two buttons are for uploading the genome assembly file and the AR gene database file. SSTAR contains an easy interface with currently only four buttons. Users who want to use different AR databases (ResFinder or custom databases) need to make sure the headers have the exact same structure as the SRST2 header format. The other information in the header (right of the space) is ignored by SSTAR and not shown in this manual example. ![]() The last number (402) is a unique identifier for each single variant. The first number (92) is a unique identifier for each AR gene group. The AR gene family is between the first and second double underscore (CMY_Bla) and the variant is between the second and third double underscore (CMY-37). The format of each AR gene FASTA header is structured like the below example: Two AR database files are included with SSTAR, a SRST2 modified ARG-ANNOT database and a SRST2 modified Resfinder database. SSTAR is developed in a certain way so it can handle the ‘SRST2 database header’ format. One needs two input files for SSTAR to run: A microbial genome assembly and AR gene file, both in FASTA format. ResGANNOT is maintained by Nicholas Vlachos ( Input data Nucleotide genes were clustered using CD-HIT at 90% sequence similarity and redundant entries were discarded. We have generated an AR gene database from Resfinder and ARG-ANNOT data, called resGANNOT. A BLAST+ copy and easy installation guide of standalone BLAST can be retrieved from:.Java can be downloaded from the Oracle website at:.profile depending on your shell, and operating system Additionally, please add (using the "echo" command) two important lines to your. BLAST+ needs to be added to your PATH variable. BLAST+ can be installed anywhere and SSTAR is compatible with all BLAST+ versions.BLAST+ needs to be installed in C:\Program Files\NCBI which is the default location when following the BLAST installation steps in the installation wizard.SSTAR for Linux and OS X is compatible with JRE6 or newer and all BLAST+ versions. In order to run SSTAR under Windows you need Java Runtime Environment (JRE) 6 or newer and standalone BLAST 2.2.29+, BLAST 2.2.30+ or BLAST 2.2.31+. SSTAR combines a standalone BLASTN with a Java interface, which operates under Windows and Unix systems. Obtaining and installing SSTAR dependencies SSTAR was successfully tested under Windows 7 and Windows 10, OS X 10.9.5, and Ubuntu 14.04 LTS.Raw Java files are also available for those who want to explore the source code.Double click on this file and SSTAR will pop up on your screen Each SSTAR version is available as an executable JAR file.In your downloaded archive you will find two different SSTAR versions SSTAR can also report modifications and/or truncations in outer membrane porin genes. It is able to identify known AR genes and detect putative new variants as well as truncated genes due to internal stop codons. SSTAR enables fast and accurate antimicrobial resistance (AR) surveillance from Whole Genome Sequencing (WGS) data. Obtaining and installing SSTAR dependencies.Manual for Sequence Search Tool for Antimicrobial Resistance (SSTAR), version 1.1.01 Table of Contents
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