Summary
I. RNA@ installation and usage
I.1. Simple exection in Command Line
I.2. Simple exection with GUI
I.3. Installation in LINUX system
I.4. LINUX - Installation as web service
II. RNA@Update
II.1 Database update from NCBI
II.2 Database update from another database
II.3 Database update from a RNA list for a specific genome
III. RNA@Experiment
III.1 RNA Experiment
I. RNA@ installation and usage
I.1. Simple exection in Command Line
In RNA@ uncompressed directory, run "./rnaat" (Linux) or rnaat.bat (Windows)
Usage:
./rnaat <options> <srcfile> <destfile>
Options:
The format for <srcfile> must be a fasta, gb or embl. Use the extension .fasta, .faa, .fa, .fna, .gb or .embl
-t annotating transfer RNA
-m annotating messenger RNA
-r annotating ribosomal RNA
-tm annotating transfer-messenger RNA
-nc annotating none-coding RNA
-misc annotating miscellaneous RNA
-all annotating all RNA
-prefixe [prefixe size] (default 15) determines the prefix size used to encode the FSM
-exportCDS export as CDS (default as an EMBL file)
Example:
./rnaat -t -r -exportCDS workspace-example/ERR2348864.fasta workspace-example/ERR2348864.cds
The command will annotate both rRNAs and tRNAs in the genome ERR2348864.fasta and export the results as ERR2348864.cds.
I.2. Simple exection with GUI
In RNA uncompressed directory, run "./rnaat-ui" (Linux) or "rnaat-ui.bat" (Windows)
I.3. Installation in LINUX system
i. In RNA uncompressed directory, execute "sudo ./install-rnat"
ii. Execute "rnaat" to run RNA@ in command line with the usage specified in I.
iii. run "rnaat-ui" to run RNA@ for GUI mode
I.4. LINUX - Installation as a web service
i. Install apache2 (consult the documention for your specific OS)
ii. Install php (consult the documention for your specific OS)
iii. In RNA uncompressed directory, execute "sudo ./install-rnat-as-webservice"
iv. The parameters upload_max_filesize and post_max_size parameter in php.ini file (usually /etc/php/php.ini or /etc/php/X.Y/apache2/php.ini where X.Y is the PHP version) may need to be altered to enable the upload of complete genomes
The default values may to be 2M and 8M. We recommand the values:
upload_max_filesize=20M
post_max_size=22M
After changing these values, apache2 must be restarted by the command "sudo /etc/init.d/apache2 restart"
v. RNA@ must be accesible at http://localhost/rnaat.html
II. RNA@Update
II.1 Database update from NCBI
WARNING: we recommand to download the last database update at rnaat.ufpa.br instead. The update take several hours and download a huge number of files from the NCBI servers. To install a donwloaded version of the database, substitue “/usr/share/rnaat/data/bd” if RNA@ is installed in your system, or “./data/bd” if you use it as a local version, by the uncompressed downloaded database file.
Usage:
./rnaat-update <dest_dir>
Options:
<dest_dir> may be “/usr/share/rnaat/data/bd” if RNA@ is installed in your linux system, or “data/bd” if you upgrade a local version of RNA@. It can also be any other directory, whereas RNA@ will not reached automatically this new database in such a case.
If interrupted, the process should restart where it stopped.
Some genomes may be “quarantined” because they contain an abnormal amount of RNAs. Consult the quarantined genome list at the end of the process at <dest_dir>/quarantined. If you think that the RNA list for some of these genomes is correct, you can include them manually (see II.3).
II.2 Database update from another database
WARNING: the database must be a FASTA file containing only one specific type of RNA
Usage:
./rnaat-update -database=[type] -src=<source_file> <dest_dir>
Options:
[type] is one of the RNA type among: the list: rRNA, tRNA, mRNA, ncRNA, misc_RNA, tmRNA
<source_file> is the database source of the new RNAs
<dest_dir> the database that will be upgrade from <source_file>. It may be “/usr/share/rnaat/data/bd” if RNA@ is installed in your linux system, or “data/bd” if you upgrade a local version of RNA@. It can also be any other directory, whereas RNA@ will not reached automatically this new database in such a case.
Example:
./rnaat-update -database=tRNA -src=workspace-example/archaeal-trnas.fa data/bd
It will upgrade the existing data/bd/tRNA.fasta file with the tRNA contained in archaeal-trnas.fa (it does not increase duplicated tRNA).
II.3 Database update from a RNA list for a specific genome
WARNING: the RNA list must be a fasta file and every CDS description must have a “gbkey” tag. For instance see the file workspace-example/GCA_003203655.1_ASM320365v1_rna_from_genomic.fna
Usage:
./rnaat-update -src=<source_file> <dest_dir>
Options:
<source_file> is the RNA list
<dest_dir> the database that will be upgrade from <source_file>. It may be “/usr/share/rnaat/data/bd” if RNA@ is installed in your linux system, or “data/bd” if you upgrade a local version of RNA@. It can also be any other directory, whereas RNA@ will not reached automatically this new database in such a case.
Example:
./rnaat-update -src=workspace-example/GCA_003203655.1_ASM320365v1_rna_from_genomic.fna data/db
It will update the database (data/db/tRNA.fasta, data/db/rRNA.fasta, etc.) with the RNAs contained into the file GCA_003203655.1_ASM320365v1_rna_from_genomic.fna (it does not increase duplicated tRNA).
III. RNA@Experiment
III.1 RNA Experiment
RNA Experiment download deposited genomes from a list with the following format:
“[genome name 1];[genome ncbi repository url 1]
[genome name 2];[genome 2 ncbi repository url 2]
...
[genome name n];[genome 1 ncbi repository url n]”
(see workspace-example/expe.txt as example). After downloading, it annotates the genome with RNA@ and compare each result with the RNA effectivelly deposited in the NCBI repository. It then generates a result directory (see files workspace-example/EXPE/result.csv and workspace-example/EXPE/html/result.html)
Usage:
./rnaat-expe <genome_list> <dest_dir>
Options:
<genome_list> is the genome list that will be processed
<dest_dir> the directory that will receive the result
Example:
./rnaat-expe workspace-example/expe.txt workspace-example/EXPE
