Input Dataset
Welcome to multiPrime - Your Ultimate targeted sequencing Software! mulitPrime1: A streamlined pipeline engineered for comprehensive target sequence detection through targeted sequencing. It accepts FASTA files and subsequently provides a curated primer set. Detailed file descriptions at https://github.com/joybio/multiPrime. multiPrime2: An advanced degenerate primer design software, which incorporates the degenerate primer design module of multiPrime1 while introducing a new global optimum algorithm. It accepts multiple alignment files, and return a candidate primer list. You can find detailed file descriptions at https://github.com/joybiomultiPrime2-GUI.
Enter the DNA sequences with FASTA format:
Input Dataset:
Please input data with the same format as example data. Total process analysis: a FASTA file is a text-based file format commonly used in bioinformatics to store nucleotide sequences. It consists of a header line starting with a ">" symbol, followed by one or more lines of sequence data. The header line typically contains information about the sequence, such as its name or identifier. The sequence data can be represented using the standard IUPAC codes for nucleotides (A, T, G, C). 
Or upload your fasta file:
Upload a file:
Drop file here or click to upload
    If your file size is larger than 1.5GB, the website will not provide automatically format checking service, then Please ensure that your data ends with [.fa] and adheres to the format specified on the left. Example file
      Classification and Sampling
    identity  :
    Seq_number_ANI  :
    ani  :
    drop  :
    max_seq  :

    About
    MultiPrime1 is a pipeline designed for broad-spectrum detection of target sequences using targeted sequencing. It is implemented in Python and Snakemake and takes a FASTA format file as input. The pipeline has three main steps: classification by identity, primer design, and primer set combination. In the classification step, redundant sequences are removed and clusters are formed by identity. Rare sequence clusters are compared to others by average nucleotide identity, and if they are deemed similar enough, they are merged. In the primer design step, multi-alignment is performed using MUSCLE or MAFFT, and candidate primers are designed using the nearest-neighbor model. Primer pairs are selected based on PCR product length, melting temperature, dimer examination, coverage with errors, and other factors. Finally, a greedy algorithm is used to combine primer pairs into a minimal primer set according to dimer examination.
    MultiPrime2 is an innovative degenerate primer design program. It proposed a solution for achieving max coverage and minimal degeneracy degenerate primer design with errors. This program is designed to create primers or primer pairs for multiple alignment files, providing users with the ability to obtain extensive and high-coverage degenerate primers tailored for specific targets.

    Protocal
    multiPrime1:

    multiPrime2:


    Download
    multiPrime v2 offers high coverage and is scalable to handle thousands of sequences. It incorporates the original multiPrime1 while introducing a new global optimum algorithm.multiPrime1：
    • The multiPrime1 module employs a nearest neighbor model to design degenerate primers, utilizing a local optimum strategy.
    • It operates very quickly, and the running time remains unaffected by the maximum degenerate number chosen.
    multiPrime2：
    • The multiPrime2 module employs a global optimum strategy to generate primers with maximum coverage.
    • The running time of multiPrime2 increases as the maximum degenerate number is raised.
    For cases where the maximum degenerate number is less than 4, both multiPrime1 and multiPrime2 demonstrate similar running times and primer coverage. However, when the maximum degenerate number exceeds 4, multiPrime2 demonstrates superior primer coverage compared to multiPrime1. However, it is important to note that the trade-off for this enhanced coverage is a longer running time in multiPrime2 compared to multiPrime1. Overall, multiPrime v2 offers users the flexibility to choose between multiPrime1 and multiPrime2 based on their specific requirements. While multiPrime1 is preferred for its fast execution, multiPrime2 excels in achieving greater primer coverage at the expense of longer running times, especially when dealing with higher degenerate numbers. Users should consider this factor while selecting the appropriate algorithm based on their specific needs and priorities.
    Name
    download
    multiPrime2-GUI.zip

    Contact us
    The project was conceptualized and scripted by Junbo Yang. Please send comments, suggestions, bug reports and bug fixes to 1806389316@pku.edu.cnyangjunbo_hi@126.com

    Citation
    Xia, Han, Zhang, Zhe, Luo, Chen, Wei, Kangfei, Li, Xuming, Mu, Xiyu, Duan, Meilin, et al. 2023. "MultiPrime: A Reliable and Efficient Tool for Targeted Next-Generation Sequencing.” iMeta e143. https://doi.org/10.1002/imt2.143

    Global Visitors
    MultiPrime revolutionizes target next-generation sequencing (targeted sequencing) by seamlessly integrating primer design theory with advanced error handling techniques and empirical compatibility examination. It lead to a remarkable improvement in the accuracy, specificity and capacity of targeted sequencing.

    © 2023 | Contact us: yang_junbo_hi@126.com
    This website is free and open to all users and there is no login requirement.