3. Workplace Apps

3.1. Blast

Introduction

I5K BLAST Tutorial is on https://i5k.nal.usda.gov/content/blast-tutorial

3.1.1. Install & Configuration

Install BLAST and append Blast_bin directory in environment variable PATH.

3.1.2. BLAST DB Configuration

There are five tables for creating BLAST DB and browsing in I5K-blast.

  • Add Organism:
    • Display name should be scientific name.
    • Short name are used by system as a abbreviation.
    • Descriptions and NCBI taxa ID are automatically filled.
_images/add_organism.png
  • Add Sequence types:
    • Used to classify BLAST DBs in distinct catagories.
    • Provide two kinds of molecule type for choosing, Nucleotide/Peptide.
  • Add Sequence
  • Add BLAST DB
    • Choose Organsim
    • Choose Type (Sequence type)
    • Type location of fasta file in FASTA file path
    • Type Title name. (showed in HMMER page)
    • Type Descriptions.
    • Check is shown, if not check, this database would show in HMMER page.
    • Save
_images/add_blastdb.png
  • Add JBrowse settings

3.2. Hmmer

HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

I5K HMMER Tutorial is on https://i5k.nal.usda.gov/webapp/hmmer/manual.

3.2.1. Install & Configuration

Install HMMER and append HMMER_bin directory in evironment varialbe PATH.

3.2.2. HMMER DB Configuration

Like Blast, HMMER databases must be configured then they could be searched.

Go django admin page and click Hmmer on left-menubar. You need to create HMMER db instance (Hmmer dbs) for each fasta file.

  • Choose Organsim
  • Type location of peptide fasta file in FASTA file path
  • Type Title name. (showed in HMMER page)
  • Type Descriptions.
  • Check is shown, if not check, this database would show in HMMER page.
  • Save
_images/hmmer_add.png

3.2.3. HMMER Query Histroy

HMMER query histories are stored in table HMMER results. Users could review them on dashboard. All query results (files on disk) will be removed if it’s expired. (default: after seven days)

Query results locate in directory $MEDIA_ROOT/hmmer/task/.

3.3. Clustal

ClustalW is the oldest of the currently most widely used programs for multiple sequence alignment. Clustal Omega is the latest version of CLUSTAL series. ClustalO is faster and more accurate because of new HMM alignment engine.

I5K CLUSTAL Tutorial is on https://i5k.nal.usda.gov/webapp/clustal/manual.

3.3.1. Install & Configuration

Install Clustalw and Clustal Omega. Then append both bin directory in evironment varialbe PATH.

3.3.2. Clustal Query Histroy

Clustal query histories are stored in table Clustal results. Users could review them on dashboard. All query results (files on disk) will be removed if it’s expired. (default: after seven days)

Query results locate in directory $MEDIA_ROOT/clustal/task/.

3.4. Dashboard

Personal query history.

3.5. Data

Rest framework. Not finished

3.6. Proxy

For providing indirect access to some resources without https. Currently it is used by Web Apollo instances for looking up GO Terms.

3.7. Drupal_SSO

Coonection to Drupal summit data function.

DRUPAL_URL = 'https://gmod-dev.nal.usda.gov'

# cookie can be seen in same domain
DRUPAL_COOKIE_DOMAIN=".nal.usda.gov"

3.8. WebApollo SSO

Complete introduction locate in Section 4.