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NAMS walkthrough example

Below is the step by step instruction on how to use our webserver as well as install and run stand-alone NAMS on a x86_64 Linux/Unix server.
For more details please refer to README file in the package.

Use the webserver

The NAMS webserver only requires the users to input the sequence (in FASTA format) of their transcript and output the coding potential prediction as well as functional annotations of the given transcript. Note that currently the users are allowed to input 1 transcript in each query.

To use the webserver, input (or copy and paste) the sequence to the textbox and click the "GO NAMS" button. We provided two testing trancripts (1 mRNA and 1 lncRNA) and the user could click the "example mRNA" and "example lncRNA" buttons to use them. The other button "clear content" was designed to clear all the data in the text box if the user needs to clean up and input another sequence.

When the user finishes inputting the transcript sequence, click the "GO NAMS" button to submit the query. The webserver will return an acknowledgement page which contains a unique job ID and jumps to the result page in 10 seconds automatically. The result page contains the coding potential prediction result and functional annotations of the query transcript (homologue search results for mRNAs and predicted secondary structure for lncRNAs). As examples, here are the result pages for the example mRNA and example lncRNA.

The result of each query will be kept on the webserver for 1 month. The users could bookmark the URL of the result page (which contains the job ID) to view it later or share with their colleagues.

Install NAMS

  1. Download the NAMS stand-alone package here or use the following command:

        $ wget http://sunlab.cpy.cuhk.edu.hk/NAMS/data/NAMS-latest.tar.gz

  2. Uncompress the package:

        $ tar zxf NAMS-latest.tar.gz

  3. A sub-directory named NAMS-latest will be created. All the required programs and data are included in this directory.

  4. Change to this directory:

        $ cd NAMS-latest

Run NAMS

In order to facilitate the process, we have provided a test dataset which contains a sub-list of transcripts in the stand-alone package under the testing_dataset/ directory.

To run NAMS on this testing dataset:

        $ ./run_testing_dataset.sh

The output should be like:

This script is used to demonstrate how to run NAMS on the test datasets.
There are two test datasets: "TAIR10.ncRNA.fa" and "TAIR10.mRNA.fa" both under the "testing_dataset" directory.

Run NAMS on the "TAIR10.ncRNA.fa":
Command line: ./NAMS testing_dataset/TAIR10.ncRNA.fa testing_dataset TAIR10.ncRNA
***** WARNING: Directory testing_dataset exists! *****
========== NAMS start: Mon Aug 12 13:33:41 HKT 2019 ==========
Step 1: Size filter
Step 2: ORF filter
Step 3: Homolog filter
Step 4: Publish results.
========== NAMS end:   Mon Aug 12 13:52:04 HKT 2019 ==========
The Output files are "testing_dataset/TAIR10.ncRNA.classification" and "testing_dataset/TAIR10.ncRNA.stat".

Run NAMS on the "TAIR10.mRNA.fa":
Command line: ./NAMS testing_dataset/TAIR10.mRNA.fa testing_dataset TAIR10.mRNA
***** WARNING: Directory testing_dataset exists! *****
========== NAMS start: Mon Aug 12 13:52:04 HKT 2019 ==========
Step 1: Size filter
Step 2: ORF filter
Step 3: Homolog filter
Step 4: Publish results.
========== NAMS end:   Mon Aug 12 14:04:22 HKT 2019 ==========
The Output files are "testing_dataset/TAIR10.mRNA.classification" and "testing_dataset/TAIR10.mRNA.stat".

This testing dataset contains 500 coding transcripts and 500 non-coding transcripts obtained from the TAIR project. Please refer to README file for more information on how to run NAMS.


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