Using TUIT

Using TUIT

Prior to using tuit for taxonomic identification, consider the settings in properties.xml and modify the available parameters if needed.

Pay attention to these two:

<BLASTNPath path= "blastn" />

<TMPDir path= "tmp" />

correct the path values to correct system paths to blastn(.exe) executables and the temporary folder that you decided to dedicate for tuit temporary files.

Open the terminal window and type:

$:>java -jar {path to}/tuit.jar -p {path to}/properties.xml -i {path to input file.fasta}

optionally you can specify the output file

$:>java -jar {path to}/tuit.jar -p {path to}/properties.xml -i {path to input file.fasta} -o {path to output file.tuit}

as well as you may decide to get a more verbose output with a “–v” flag

$:>java -jar {path to}/tuit.jar -p {path to}/properties.xml -i {path to input file.fasta} -o {path to output file.tuit} -v

the later will create a log file to help better understand how the algorithm parsed the blast output. TUIT will perform a BLASTN homology search and then use the output for classification.

You can always specify a pre-blasted xml-formatted output, which you decide to use as source for classification

$:>java -jar {path to}/tuit.jar -p {path to}/properties.xml -b {path to blast_output.xml} -i {path to input file.fasta} -o {path to output file.tuit} -v

Note that you still need to specify the query input file for that particular blast. Оtherwise the algorithm would not be able to correctly identify the sequences form the query with the output.

Using the taxonomic database

If you are conducting a research that involves classification of unknown nucleotide sequences, chances are that you could benefit from a “quick lookup” for NCBI taxid for a certain taxonomic group. The “f_level_children_by_parent” view from the tuit taxonomic database could come handy. You can use the “tuit@localhost” MySQL user to login and perform searches manually or with a script.

mysql:> select * from f_level_children_by_parent where name=’Homo sapiens’ will show a row like this:

'9605',	'9606',	'Homo sapiens',	'species',
Parent taxid	taxid	Scientific name	Taxonomic rank