Powerful Accurate Open Access

Design Genome-Wide
Primers with Confidence

GenPrimeX is a comprehensive web-based platform for genome wide primer design. PCR Primers enable precise amplification of target nucleotides, forming the basis for genetic analysis, molecular identification and diagnostics.

Get Started Explore Modes

Free | Open Access | Open for All Researchers

Genome / Sequence

A T G C A T G C A T

SSR Motif

5′ → Forward Primer → 3′

3′ ← Reverse Primer ← 5′

✦ Annotation Aware

📄

Genome
Input

→

🔁

SSR
Detection

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🔬

Primer
Design

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📊

Research
Grade

→

📥

Export
Ready

✓ High Accuracy ✓ Privacy First ✓ Built for Research

Hover any element to learn more

WORKFLOWS

Mode 1 — FASTA Only

SSR/Microsatellite Repeat Analysis

Design primers directly on FASTA sequences without specific SSR targeting. Ideal for general genome-wide primer design with fast processing.

Files Needed: FASTA

Mode 2 — FASTA + MISA

Genome-Wide Primer Design

Design primers flanking SSR regions identified by MISA. Perfect for SSR marker development and population genetics studies.

Files Needed: FASTA MISA Catalog

Mode 3 — Full Annotation

Combined SSR Analysis + Primer Design

Complete SSR annotation with genomic context. Includes GFF and functional annotations (GO terms) for comprehensive analysis.

Files Needed: FASTA MISA GFF Annotation

Open Access Platform

GenPrimeX is freely accessible to all users worldwide — academic, non-profit, and commercial organizations. No registration or licensing fees. Start designing primers immediately!

Start Now →

Primer Design Engine

SSR Entries per Run

60K+

Export Results

TSV

Trusted By

Researchers Worldwide

Live Usage Statistics

●Updates every 30 seconds

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Choose Your Workflow

Select the mode that best fits your input data and analysis requirements

FASTA Only

Design primers directly on FASTA sequences without specific SSR targeting. Ideal for general primer design.

Features:

Upload: FASTA file only
Customizable product size range
Multiple primer pairs per sequence
Fast processing

Start Mode 1 →

FASTA + MISA

Design primers flanking SSR regions identified by MISA. Perfect for SSR marker development.

Features:

Upload: FASTA + MISA catalog
Primers flank SSR regions
SSR motif information included
Marker-ready output

Start Mode 2 →

Full Annotation

Complete SSR annotation with genomic context. Includes GFF and functional annotations.

Features:

Upload: FASTA + MISA + GFF + Annotation
SSR location (exon/intron/UTR)
Functional annotation included
Comprehensive analysis

Start Mode 3 →

Bioinformatics Tool — ICAR-NBFGR

About GenPrimeX

GenPrimeX (Genome Wide Primer eXplorer) is a comprehensive bioinformatics web platform engineered for genome-scale SSR marker discovery and primer design. Built on Primer3 and MISA, it integrates FASTA sequences, microsatellite catalogs, and genomic annotation to deliver publication-ready primer outputs across three configurable workflows.

Primer3 Engine MISA Integration GFF Annotation TSV Export 3 Analysis Modes Open Access

ICAR-National Bureau of Fish Genetic Resources (NBFGR) Lucknow, Uttar Pradesh, India · Under the (Indian Council of Agricultural Research)

Integrated Analysis Pipeline

From raw genome sequence to annotated, publication-ready primers in one unified workflow

FASTA

Genome
Sequence

→

MISA

SSR
Detection

→

GFF

Genomic
Annotation

→

GenPrimeX

Core
Engine

→

Primer3

Design
Engine

→

Results

TSV
Output

Mode 1 uses FASTA only Mode 2 adds MISA catalog Mode 3 integrates full GFF annotation

High-Throughput Speed

Processes genome-wide SSR loci with Primer3 in seconds. Batch-ready for large genomes with thousands of candidate sites.

Quality-Filtered Primers

Each primer pair is validated for Tm, GC%, product size, and specificity — parameters tuned to your target species.

3 Configurable Modes

From simple FASTA-only runs to fully annotated GFF-integrated analysis — choose the mode that matches your data availability.

Annotation-Aware Results

Mode 3 maps each SSR primer to its genomic feature — gene, exon, intron, or UTR — with functional annotation and GO terms.

Multi-Format Export

Download results as tab-separated TSV files — ready for MEGA, PopGenome, or any population genetics pipeline.

Open Access Globally

No paywalls, no license restrictions. Freely usable by academic, non-profit, and commercial researchers worldwide.

Mode Comparison Matrix

Capability	Mode 1	Mode 2	Mode 3
FASTA genome input
MISA SSR catalog (.misa)	—
GFF3 genome annotation	—	—
Functional annotation (GO, product)	—	—
SSR-flanking primer design	—
Genome-wide bulk analysis
Processing speed	Fast	Medium	Comprehensive

Open Access — Free for Everyone GenPrimeX is freely accessible to all users — academic institutions, non-profit organizations, and commercial entities worldwide. No license fees, no registration barriers.

Team Members

ICAR- National Bureau of Fish Genetic Resources (NBFGR-Component), Lucknow, India

1. Coordinator CRP Genomics

Name	Dr. Joykrushna Jena
Designation	Deputy Director General
Email	Ddgfs.icar@gov.in

2. Principal Investigator (PI)

Name	Dr. Rajeev K. Singh
Designation	Principal Scientist & Head
Division	Germplasm Exploration, Evaluation Conservation
Email	rajeevsingh1@yahoo.com

3. Co-Principal Investigator (Co-PI)

Name	Dr. Labrechai Mog Chowdhury
Designation	Scientist
Division	Germplasm Exploration, Evaluation Conservation
Email	mogbiotech123@gmail.com

4. Research Scholar

Name	Shriti Shreya
Designation	Young Professional II
Division	Germplasm Exploration, Evaluation Conservation
Email	s7.shriti@gmail.com

Contact

Sr.	Name	E-mail	Phone
1	Dr. Joykrushna Jena Coordinator CRP Genomics, Deputy Director General (Fisheries Science) Division of Fisheries, Krishi Anusandhan Bhawan - II, New Delhi - 110 012 INDIA	ddgfs@icar.gov.in jkjena2@gmail.com	+91-11-25846738, 91-11-25842284/85/62/70/71 Ext. 1309 Fax: 91-11-25841955
2	Dr. Kajal Chakraborty Director, ICAR-National Bureau of Fish Genetic Resources Canal Ring Road, P.O. Dilkusha, Lucknow - 226 002 INDIA	director.nbfgr@icar.gov.in	+91-522-2441735, 2440145 Fax: +91-522-2442403
3	Dr. Rajeev K. Singh Principal Scientist & Head, ICAR-National Bureau of Fish Genetic Resources Canal Ring Road, P.O. Dilkusha, Lucknow - 226 002 INDIA	rajeevsingh1@yahoo.com	+91-9415164176

🧬

Bioinformatics — Learn the Concepts

Explore the core concepts behind GenPrimeX through curated resources from trusted scientific databases.

✔ Curated scientific links ✔ NCBI, NHGRI & more ✔ GenPrimeX workflow guide

Primer

National Human Genome Research Institute (NHGRI) — genome.gov

Polymerase Chain Reaction (PCR)

National Human Genome Research Institute (NHGRI) — genome.gov

Primer-BLAST

National Center for Biotechnology Information (NCBI) — ncbi.nlm.nih.gov

Primer3

University of Tartu — primer3.ut.ee

Microsatellite

National Human Genome Research Institute (NHGRI) — genome.gov

Simple Sequence Repeat (SSR)

National Human Genome Research Institute (NHGRI) — genome.gov

MISA — MicroSAtellite Identification Tool

IPK Gatersleben — webblast.ipk-gatersleben.de

Tandem Repeats Finder

Boston University — tandem.bu.edu

FASTA Sequence Format

National Center for Biotechnology Information (NCBI) — ncbi.nlm.nih.gov

GFF / GTF Format

Ensembl Genome Browser — ensembl.org

Gene Ontology (GO)

Gene Ontology Consortium — geneontology.org

NCBI Genome Datasets

National Center for Biotechnology Information — ncbi.nlm.nih.gov

🔄 The Complete GenPrimeX Pipeline

🚦 Choosing Your Mode — What Goes In, What Comes Out

Mode 1 — FASTA Only

Best for: General primer design across whole genome sequences. No SSR targeting.

Input:

FASTA file only

Output contains:

Primer sequences (forward & reverse)
Tm, GC%, product size for each primer
Primer position on each sequence

Mode 2 — FASTA + MISA

Best for: Designing SSR markers. Primers are designed to flank each microsatellite.

Input:

FASTA + MISA catalog

Output adds:

SSR motif and repeat number
Exact SSR start/end position
Primers flanking each SSR

Mode 3 — Full Annotation

Best for: Complete genomic context — know exactly which gene your SSR is in and what that gene does.

Input:

FASTA + MISA + GFF + Annotation

Output adds:

SSR location: exon / intron / UTR / intergenic
Associated gene ID and description
GO terms (biological function)

📊 Understanding Your Results — Column by Column

Basic columns (all modes):

Sequence_ID — which chromosome/contig the SSR/primer is on

Primer_Left / Primer_Right — the actual DNA sequence of each primer (what you order from the lab)

Product_Size — how large the amplified region will be (in base pairs)

Tm_Left / Tm_Right — melting temperature of each primer (°C)

GC_Left / GC_Right — GC% of each primer

Mode 2 & 3 additions:

SSR_Motif — the repeat unit (e.g., GA, ATG)

SSR_Repeat — how many times the motif repeats

SSR_Start / SSR_End — position of the SSR in the sequence

Mode 3 only:

Genomic_Region — exon / intron / 5'UTR / 3'UTR / intergenic

Gene_ID — the gene the SSR falls in

Gene_Description — what protein/function the gene encodes

GO_Terms — Gene Ontology terms for biological function

🚀 Ready to Start? Here's Your Step-by-Step Guide

Prepare your FASTA file — Make sure it's a valid FASTA file with your organism's DNA sequences. Accepted formats: .fa, .fasta, .fna, .txt

Choose your mode — Have only a FASTA? Use Mode 1. Have MISA output too? Use Mode 2. Have all 4 files? Use Mode 3 for complete annotation.

Upload your files & set parameters — Set desired product size range, min repeat counts, and Primer3 settings. Defaults work well for most studies.

Submit and wait — GenPrimeX will run the analysis. Large genomes (thousands of SSRs) may take several minutes.

Download results — Get your TSV file containing all primer pairs with full annotation details. Ready for your publication!

Start with Mode 1 → Full Annotation (Mode 3) →

✅ You're now a GenPrimeX Expert!

Mode 1 (FASTA only) → general primers for any sequence

Mode 2 (FASTA + MISA) → SSR-flanking primers for marker development

Mode 3 (all 4 files) → primers + genomic region + gene function = complete picture

GenPrimeX

Design Genome-Wide
Primers with Confidence

WORKFLOWS

SSR/Microsatellite Repeat Analysis

Genome-Wide Primer Design

Combined SSR Analysis + Primer Design

Open Access Platform

Live Usage Statistics

Choose Your Workflow

FASTA Only

Features:

FASTA + MISA

Features:

Full Annotation

Features:

About GenPrimeX

Team Members

Contact

Citation

Bioinformatics — Learn the Concepts

Primers

SSR Markers

Annotation Files

GenPrimeX Workflow

🔄 The Complete GenPrimeX Pipeline

🚦 Choosing Your Mode — What Goes In, What Comes Out

📊 Understanding Your Results — Column by Column

🚀 Ready to Start? Here's Your Step-by-Step Guide

✅ You're now a GenPrimeX Expert!

Design Genome-Wide Primers with Confidence

WORKFLOWS

SSR/Microsatellite Repeat Analysis

Genome-Wide Primer Design

Combined SSR Analysis + Primer Design

Open Access Platform

Live Usage Statistics

Choose Your Workflow

FASTA Only

Features:

FASTA + MISA

Features:

Full Annotation

Features:

About GenPrimeX

Team Members

Contact

Citation

Bioinformatics — Learn the Concepts

Primers

SSR Markers

Annotation Files

GenPrimeX Workflow

🔄 The Complete GenPrimeX Pipeline

🚦 Choosing Your Mode — What Goes In, What Comes Out

📊 Understanding Your Results — Column by Column

🚀 Ready to Start? Here's Your Step-by-Step Guide

✅ You're now a GenPrimeX Expert!

Design Genome-Wide
Primers with Confidence