Annocript

Description

annocript website  

Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes blast analysis with UniProt, NCBI Conserved Domain Database and Nucleotide division adding also annotations from Gene Ontology, the Enzyme Commission and UniPathways. Annocript also gives information about the longest ORF and the non-coding potential using external software. Annocript is also capable to identify putative long non-coding RNAs by using an heuristic based on homology and sequence features.

Environment Modules

Run module spider annocript to find out what environment modules are available for this application.

System Variables

• HPC_{{#uppercase:annocript}}_DIR - installation directory
• HPC_{{#uppercase:annocript}}_BIN - executable directory
• HPC_{{#uppercase:annocript}}_CONF - config directory

Additional Information

Start by copying the config.

cp $HPC_ANNOCRIPT_CONF/config_user.txt .

Next, you must create a personal database with annocript_<username>_<project> where <project> is a word that identifies a particular project. After creating the database edit the config_user.txt with the new name and password for your database.

Citation

If you publish research that uses annocript you have to cite it as follows:

Musacchia F, Basu S, Petrosino G, Salvemini M, Sanges R. Annocript: a flexible pipeline for the annotation of transcriptomes which can also identify putative long non-coding RNA