Malakite: An Automatic Tool for Characterisation of Structure of Reliable Blocks in Multiple Alignments of Protein Sequences

J Bioinform Comput Biol. 2010 Jun;8(3):503-17. doi: 10.1142/s0219720010004720.

Abstract

It makes sense to speak of alignment of protein sequences only within the regions, where the sequences are related to each other. This simple consideration is often disregarded by programs of multiple alignment construction. A package for alignment analysis MAlAKiTE (Multiple Alignment Automatic Kinship Tiling Engine) is introduced. It aims to find the blocks of reliable alignment, which contain related regions only, within the whole alignment and allows for dealing with them. The validity of the detection of reliable blocks' was verified by comparison with structural data.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Amino Acid Sequence
  • Molecular Sequence Data
  • Proteins / chemistry*
  • Sequence Alignment / methods*
  • Sequence Analysis, Protein / methods*
  • Software*

Substances

  • Proteins