Frequently Asked Questions (FAQs)

  • blastp
  • Database: swissprot
  • Input: fasta_file.seq
  • Alignments: 500
  • Word size: 6

What settings are used for COBALT to create the MSA (Multiple Sequence Alignment)?

  • Output format: mfasta
  • End gap open penalty: 5
  • End gap extend penalty: 1
  • Gap open penalty: 11
  • Gap extend penalty: 1
  • BLAST e-value: 0.003
  • No RPS: T
  • Tree method: clust

Can I use MoNvIso without an internet connection?

No, MoNvIso requires an internet connection to access necessary databases like UniProt and PDB.

What species' proteins can be modeled?

Currently, MoNvIso only models proteins belonging to Homo sapiens as extracted from the UniProt database.

How can I cite MoNvIso?

Please cite MoNvIso as follows:

Oliva, F., Musiani, F., Giorgetti, A., De Rubeis, S., Sorokina, O., Armstrong, D. J., Carloni, P., & Ruggerone, P. (2023). Modelling eNvironment for Isoforms (MoNvIso): A general platform to predict structural determinants of protein isoforms in genetic diseases. Frontiers in chemistry, 10, 1059593. https://doi.org/10.3389/fchem.2022.1059593