MorphoCatcher ATCGGCATTCTGCA ***---**---***

New Project


Catching polymorphisms


Key software applications

Target screening

Fast and automatic online tool to screen for most suitable diagnostic targets in genomes using novel sliding-window approach

Alignment processing

Masking all taxon-specific polymorphisms, insertions and deletions directly in multiple sequence alignment of orthologs

Data inspecting

Complete set of input and output files including publication-quality plots is available for download and further analysis


Research case stories



Plant pathogen detection


Pipeline for users

  • DNA.png

    Export target sequences

    The user should to prepare a set of any potential targets in genome of interest, for example highly conserved genes or regions

  • Chart.png

    Find closest homologs

    To catch statistically reliable mutations, it is necessary to find closest orthologs for the target of interest using NCBI BLAST

  • Editor.png

    Make multiple alignment

    Each set of pre-formatted orthologous target sequences is submitted to Clustal Omega with an "Input" value of the order option

  • Sliders.png

    Detect specific mutations

    Multiple sequence alignment of orthologous sequences is submitted to MorphoCatcher in accordance with type of operating system

  • Idea.png

    Design primer sets

    Output text files with masked target sequence for each taxon can be directly submitted to PrimerExplorer

  • Manual.png

    Manual and tutorial files

    The user can to download a detailed manual with two case studies, tutorial files, and a command line version of the tool here


Authors and developers


Fedor V. Shirshikov

Algorithm developer


Yury A. Pekov

Python coder


Konstantin A. Miroshnikov

Scientific advisor

We hope that future versions of the MorphoCatcher will automatize some steps from the pipeline to provide high-throughput target screening and processing. If you have any further questions, please do not hesitate to contact our technical support at