MARS - Prot: Maintainer of Alignments using Reference Sequences for Proteins
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README.md

MARS - Prot

Maintainer of Alignments using Reference Sequences for Proteins

MARS-Prot is a maintenance tool for protein multiple sequence alignments (MSAs) that allows for the incorporating of new sequences into existing (hand-optimized) alignments.

Please see the main documentation file for information on usage, dependencies, file formats and troubleshooting.

Directory structure:

  • src - C# source code
  • mars - MARS-Prot
  • msa-comp - Tool to compare an alignment against a "gold standard"
  • DJPCommonBioinfo - Bioinformatics library that mars and msa-comp depend upon
  • bin - Windows binaries
  • doc - Documentation
  • doc/MARS_readme.pdf - Main documentation file
  • biology - Biological data
  • LacI-GalR_Expanded.fasta - Expanded alignment of the LacI/GalR transcription regulators
  • BLOSUM62.txt - BLOSUM62 similarity matrix from NIH NCBI