VARIANT

How to Upload Your Data

You need to upload 3 types of files for each virus:

Reference Genome

Complete genome sequence (.fasta)

Reference Proteome

Protein sequences (.fasta)

MSA File

Multiple sequence alignment (.txt)

Create Custom Virus

Virus Name *

Enter a unique name for your virus

Virus Type

Single-segment virus

Multi-segment virus

Custom Virus Benefits:

Upload your own virus data
No need for pre-configuration
Support for any virus type
Automatic file organization

Upload Data Files

One-click default setup for trying analysis and visualization quickly

Quick File Type

Use one click instead of opening the file type dropdown each time.

Virus Type *

Choose the virus you want to analyze

Segment (for multi-segment viruses)

Only appears for multi-segment viruses like H3N2

File Type *

Choose the type of file you're uploading

Select File *

Choose the file to upload from your computer. If file type is empty, VARIANT will try to auto-detect it.

Data Requirements

Required Files for Analysis:

Reference Genome: FASTA format (.fasta)
Reference Proteome: FASTA format (.fasta)
MSA File: Multiple sequence alignment (.txt)

What Correct Input Looks Like (Examples)

Examples only. Upload your real files above.

Reference Genome FASTA (example)

>NC_045512 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome
ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA
CGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAAC
TAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTG
TTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTC
CCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTAC
GTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG
CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGAT
GCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTC
GTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCT
TCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTA
GGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTG
TTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGG
CCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTG
TCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTG
CTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAA
ATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAA
CCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCAC
CAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCA
GACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACT
... (remaining lines omitted for brevity in this patch context)

Proteome FASTA (example)

>YP_009724390.1|spike_surface_glycoprotein|21563..25384
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHV
SGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPF
LGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPI
NLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYN
ENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASV
YAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIAD
YNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYF
PLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFL
PFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLT
PTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLG
AENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGI
AVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDC
LGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIG
VTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDI
LSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLM
SFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNT
FVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVA
KNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDD
SEPVLKGVKLHYT

MSA text/FASTA (example)

CLUSTAL O(1.2.4) multiple sequence alignment


NC_045512.2                                                        ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCT	60
hCoV-19/Shanghai/SJTU-236325/2022|EPI_ISL_16327572|2022-12-19      -TTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTTGATCTCTTGTAGATCT	59
                                                                    ****************************************** ****************

NC_045512.2                                                        GTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACT	120
hCoV-19/Shanghai/SJTU-236325/2022|EPI_ISL_16327572|2022-12-19      GTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACT	119
                                                                   ************************************************************

NC_045512.2                                                        CACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATC	180
hCoV-19/Shanghai/SJTU-236325/2022|EPI_ISL_16327572|2022-12-19      CACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATC	179
                                                                   ************************************************************

NC_045512.2                                                        TTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTT	240
hCoV-19/Shanghai/SJTU-236325/2022|EPI_ISL_16327572|2022-12-19      TTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTT	239
                                                                   ************************************************************

NC_045512.2                                                        CGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAAC	300
hCoV-19/Shanghai/SJTU-236325/2022|EPI_ISL_16327572|2022-12-19      TGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAAC	299
                                                                    ***********************************************************

NC_045512.2                                                        ACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGG	360
hCoV-19/Shanghai/SJTU-236325/2022|EPI_ISL_16327572|2022-12-19      ACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGG	359
                                                                   ************************************************************

NC_045512.2                                                        AGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG	420
hCoV-19/Shanghai/SJTU-236325/2022|EPI_ISL_16327572|2022-12-19      AGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG	419
                                                                   ************************************************************

... (remaining lines omitted for brevity in this patch context)

Important Notes:

Files are organized by virus type and segment (if applicable)
Reference genomes and proteomes go to refs/ folder
MSA files go to clustalW/ folder
Upload files before starting analysis

Upload Checklist:

Reference Genome uploaded

Reference Proteome uploaded

MSA File uploaded

Start New Analysis

Analysis Configuration

Virus Type *

Genome ID (Optional)

Leave empty to process all genomes in MSA file, or specify a specific genome ID

Select a virus with all required data files uploaded to enable analysis.

Analysis in progress... This may take several minutes.

Generate Visualization

Virus Type *

Genome ID

Leave empty to process the 1st genome, or specify a specific genome ID

Select a virus with completed analysis results to generate visualizations.

This will generate all three visualization types

Visualization Types:

Mutation Analysis

Combined genome and protein mutation analysis.

Row/Hot Mutations

Visualization of row and hot mutations on protein bars.

PRF Regions

Programmed Ribosomal Frameshifting regions analysis.

Interactive Visualization

No Visualization Available

Generate a visualization above to see it here.

RNA Secondary Structure — Dual Graph Assignment

Submit an RNA secondary structure in dot-bracket notation to assign its dual graph topology ID. The pipeline converts your structure through DSSR format → CT file → dual graph library match.

Structure ID *

Used as the file base name throughout the pipeline.

Dot-Bracket Input

Format: first line = sequence, second line = dot-bracket. Use & for chain breaks.

Upload a .dbn file. The Structure ID is auto-filled from the filename.

Track Your Jobs

Enter a Job ID to check the status of a specific analysis job.

Current Job Information

Job ID:

Status: Completed

Created:

Virus:

Analysis History

Loading analysis history...

VARIANT Documentation

Viral mutAtion trackeR aImed At GeNome and proTein-level

Features

Genome Analysis

Comprehensive mutation tracking across entire viral genomes

Protein Impact

Analysis of mutations on protein structure and function

Frameshift Detection

Identification of potential ribosomal frameshifting sites

Interactive Visualizations

Generate all three visualization types with one click

Streamlined Workflow

Auto-populated virus selection
One-click visualization generation
Real-time job tracking
Automatic frameshift detection

Advanced Visualizations

Interactive HTML visualizations
Fullscreen viewing mode
Multiple visualization types
Export capabilities

Quick Start

🚀 Get Started in 4 Steps

Follow these simple steps to analyze your virus data

Step 1: Data Upload

1Go to Data Upload tab
2Select virus type (or create custom)
3Upload reference genome (.fasta)
4Upload reference proteome (.fasta)
5Upload MSA file (.txt)

Step 2: Analysis & Visualization

1Go to Analysis & Visualization tab
2Select your virus (auto-populated)
3Optional: Enter specific genome ID
4Click "Start Analysis"

Step 3: Analysis & Visualizations

1Wait for analysis completion
2Click "Generate All Visualizations"
3View all three visualization types
4Use fullscreen for detailed view

Step 4: RNA Dual Graph

1Go to RNA Dual Graph tab
2Paste dot-bracket input
3Run dual-graph assignment
4View RNA Dual Graph IDs and plot

Output Files

Results are written under result/{virus_name}/ and downloadable from History.

File Pattern	Description
`{genome_id}_mutation_summary.csv`	Position-level nucleotide and amino-acid mutation table.
`{genome_id}_row_hot_mutations.csv`	Clustered and high-frequency mutation report.
`{genome_id}.txt`	Detailed per-genome mutation text report.
`potential_PRF.csv` or `prf_analysis.prf_candidates.csv`	Candidate PRF sites from PRF scanner.

Contact

Questions or issues: rw3594@nyu.edu or GitHub.

File Requirements

Reference Genome

Format .fasta

Content Complete genome sequence

Single sequence per file
Standard FASTA format
Complete genome length

Reference Proteome

Format .fasta

Content Protein sequences

Multiple proteins allowed
Standard FASTA format
All expected proteins

MSA File

Format .txt

Content Multiple sequence alignment

ClustalW format preferred
Contains all sample sequences
Aligned sequences

How to Upload Your Data

Reference Genome

Reference Proteome

MSA File

Create Custom Virus

Custom Virus Benefits:

Upload Data Files

Data Requirements

Required Files for Analysis:

What Correct Input Looks Like (Examples)

Important Notes:

Upload Checklist:

Start New Analysis

Analysis Configuration

Job Started Successfully!

Analysis Complete!

Generate Visualization

Visualization Types:

Mutation Analysis

Row/Hot Mutations

PRF Regions

Interactive Visualization

No Visualization Available

Mutation Analysis

Row/Hot Mutations

PRF Regions

RNA Secondary Structure — Dual Graph Assignment

Dual Graph Assignment Complete

Track Your Jobs

Current Job Information

Analysis History

VARIANT Documentation

Features

Genome Analysis

Protein Impact

Frameshift Detection

Interactive Visualizations

Streamlined Workflow

Advanced Visualizations

Quick Start

🚀 Get Started in 4 Steps

Step 1: Data Upload

Step 2: Analysis & Visualization

Step 3: Analysis & Visualizations

Step 4: RNA Dual Graph

Output Files

Contact

File Requirements

Reference Genome

Reference Proteome

MSA File