Personal BLAST Navigator (PLAN) Frequently Asked Questions and Small Tutorials

0: Preface

This document contains answers to some frequently asked questions and step-by-step instructions on how to perform some basic operations in PLAN. We keep improving our documents and the list in this document is expanding. If you have any questions that are not answered here, please don't hesitate to contact the PLAN authors.

1. Q: I can't decide if a "personal project" or a "public project" is better for me...

A: A personal project, by its name, belongs to a registered person (the project owner) unless the project owner decides to publish it. Thus creating a personal project requires user registration and logging in. Operating an existing personal project also requires the project owner to log in. At any time the project owner may publish the project. By publishing the project, he/she makes the project to appear in the list of "shared personal projects" so that general visitors may open, browse and search the project data. The owner may publish the project for open access (full control), meaning any one may make any changes to the project, or for read-only access, meaning others may read the project data but may not make any changes. Even if a personal project is "published", the owner may unpublish it at any time so that the project becomes accessible to him/her only again. Personal projects have long data retention periods. We will not delete your data without your consent.

Creating a public project, on the other hand, does not require user registration or logging in. Once created, it remains in the public territory for everyone's open access (browse, search and make any changes). Public projects have short data retention periods. We may delete any public projects that are more than seven (7) days old without notification in advance.

In short, if your data is sensitive or is intended to retain for a long period, you should register and create a personal project. If you just want to utilize some of PLAN's functions quick and dirty without caring your data privacy, you may create a public project. We encourage you to delete a public project which was originally created by you right after use.

2. Q: How do I do a BLAST search on my sequences and view the results?

Create/open a project.
Make sure that your sequences are in FASTA format.
Click on the menu "Upload New Query Sequences" from the left navigation panel.
Follow the on-screen instructions to upload your sequences. Make sure you select the "Do automatic BLAST search" option for the "After Successful Upload" operation.
Wait until you see a notification on successful upload. Then follow the on-screen instructions to do BLAST search.
Follow the on-screen instructions to select a BLAST search option (available BLAST search options may vary depending on the PLAN server you are using and your user group), and submit search request.
You will get a confirmation of your search submission. Follow the onscreen instructions to go back to your project index page. On the top of the page you will see an BLAST search status window like below:
You may refresh the web page occasionally, work on other parts of your project as usual, close your project, or walk away while the search is being performed in the background. Each time you load/reload a project page or re-open the same project, the status window above will be refreshed to provide the last update on your search process.
Once the search is done, the status window will look like below:
Follow the on-screen instructions to download the result file (in NCBI plain text format).
Once the result file is successfully downloaded and archived, follow the on-screen instructions to populate the result file into database.
You are all set.

3. Q: How do I do a BLAST search on my sequences that are already uploaded to the server?

Click on the menu "List Saved Query Sequences" from the left navigation panel.
From the list, find the sequence FASTA file that you want to do BLAST search on.
Click on the corresponding "Do BLAST Search" link for the sequence file.
Follow steps 6 - 11 in FAQ #2.

4. Q: I want to first BLAST my sequences against the NCBI NT database. Then on those sequences that don't have a hit to NT, BLAST them against the Medicago EST database. How should I do?

Follow FAQ #2 to upload your sequences and BLAST against NCBI NT database, if your sequences have not been saved on PLAN server yet; or follow FAQ #3 to BLAST your saved sequences against NCBI NT database.
Once BLAST results for the above search have been populated to the database, click on the menu "Download Un-annotated Query Sequences" from the left navigation panel. Save the un-annotated query sequences to your local machine.
Follow FAQ #2 to upload your sequences downloaded from the step 2 again, and BLAST them against Medicago EST database. Note that in step 3 of FAQ #2, in the upload form, make sure you select option "Replace previous sequences in the database with new sequences in the uploaded file" for "On Duplicated Accession IDs" operation.

5. Q: The BLAST database that I would like to search against does not appear in the list. What should I do?

A: The BLAST options and databases that are available to you are controlled by the system administrator. Users in different groups may have different privileges. Please contact your system administrator to grant you an access to the designated database.

6. Q: How do I know the percentage of my query sequences that have at least one hits in the NCBI NT database with e-value <= 1e-6?

If you don't know the total number of your original query sequences: Click on the menu item "Filter BLAST Results" from the left navigation panel. In the filters form, make sure the option "Hide queries with no target (hit) that passed the above filters" is NOT checked. Apply the filters. Then click on the menu item "Summary of Search Sessions" from the left navigation panel. You will see "# of Unique Queries" listed under your BLAST results against NCBI NT database. This is the total number of unique queries that you originally submitted for search.
Repeat step 1. This time, in the filters form, make sure the option "Hide queries with no target (hit) that passed the above filters" is checked. Also make sure your e-value filter is 1e-6 and your score filter is 0. You may see the number appeared as "# of Unique Queries" changes to a lower number. This is the total number of unique queries that have hits with e-value <= 1e-6.
The number you got from step 2 over the number you got from step 1 will produce the percentage you want.