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Guide to using the Synteny Analysis Server

Quick Start Guide

Get started in 3 simple steps:

  1. Go to Create New Job - Start a new analysis
  2. Click "Load Sample" - Try our example data first
  3. Create New Job - Get your unique result link

Note: Bookmark your result link! It's the only way to access your results later.

Understanding Your Data

Input Formats Accepted:

  • TXT File: List of NCBI accession numbers (one per line)
  • TAR Archive: Gzipped tarball containing FASTA genome files
  • Parameter Files: Advanced settings for genmap, macle, and dups tools

Processing Options

Automatic Mode (Recommended):

  • Uses optimized default parameters
  • Suitable for most genome analyses
  • Faster processing time

Manual Mode (Advanced):

  • Upload custom parameter files
  • Fine-tune analysis parameters

Privacy Options:

  • Public: Results accessible via link and results table
  • Private: Password-protected access via link

Step-by-Step

Step 1: Prepare Your Data

Option A: NCBI Accessions (Easiest)

Create a text file with one accession per line:

GCA_000005825.2
GCA_000006745.1
GCA_000008865.2

Option B: Your Own Genomes

Create a gzipped tarball (.tar.gz) containing FASTA files:

tar -czf genomes.tar.gz *.fasta

Step 2: Submit Your Job

  1. Job Name: Enter a descriptive name (optional)
  2. Email: Provide email for notifications (optional)
  3. Upload Files: Choose TXT or TAR file
  4. Processing Options: Select automatic or manual mode
  5. Privacy: Choose public or private results

Step 3: Monitor Progress

  • Save the result link provided after submission
  • Check job status using the link
  • Receive email notification when complete (if email provided)

Step 4: Interpret Results

Your results will include:

  • Anchor Points: Pairwisely conserved genomic regions
  • Synteny Analysis Programs: Downstream programs for comparative genome analyses
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