Bioinformatics Toolbox

Sequence Analysis

Bioinformatics Toolbox provides sequence analysis and visualization tools for genomic and proteomic sequence data. You can perform a variety of analyses, including multiple sequence alignments and the building and interactive viewing and manipulation of phylogenetic trees.

Sequence Alignment

The toolbox provides functions, objects, and methods for sequence analysis, including pairwise sequence, sequence profile, and multiple sequence alignment. These include:

  • MATLAB implementations of standard algorithms for local and global sequence alignment, such as the Needleman-Wunsch, Smith-Waterman, and profile-hidden Markov model algorithms
  • Progressive multiple sequence alignment
  • Graphical representations of alignment results matrices
  • Standard scoring matrices, such as the PAM and BLOSUM matrix families
  • Consensus sequence calculation and sequence logo display

Sequence Utilities and Statistics

The toolbox lets you manipulate and analyze your sequences to gain a deeper understanding of your data. You can:

  • Convert DNA or RNA sequences to amino acid sequences using the genetic code
  • Perform statistical analysis on the sequences and search for specific patterns within a sequence
  • Apply restriction enzymes and proteases to perform in-silico digestion of sequences or create random sequences for test cases
  • Predict minimum free energy secondary structure of RNA sequences

Sequence Visualization

The toolbox enables you to visualize sequences and alignments. You can view linear or circular maps of sequences annotated with GenBank features. You can visualize secondary structure diagrams of an RNA sequence. Interactive viewers let you explore and modify pairwise and multiple sequence alignments.

Phylogenetic Tree Analysis

The toolbox enables you to create and edit phylogenetic trees. You can calculate pairwise distances between aligned or unaligned nucleotide or amino acid sequences using a broad range of similarity metrics such as Jukes-Cantor, p-distance, alignment-score, or a user-defined distance method. Phylogenetic trees are constructed using hierarchical linkage with a variety of techniques, including neighbor joining, single and complete linkage, and Unweighted Pair Group Method Average (UPGMA).

The toolbox supports weighting and rerooting trees, calculating subtrees, and calculating the canonical form of trees. The phylogenetic tree viewer lets you prune, reorder, and rename branches; explore distances; and read or write Newick-formatted files. You can also use the annotation tools in MATLAB to create presentation-quality trees.

Protein Feature Analysis

The toolbox provides protein sequence analysis techniques, including routines for calculating properties of a peptide sequence such as atomic composition, isoelectric point, and molecular weight. You can determine the amino acid composition of protein sequences, cleave a protein with an enzyme, and create backbone plots and Ramachandran plots of PDB data. You can use the Sequence Tool to view the properties of an amino acid sequence or use the Molecule Viewer to display and manipulate 3D molecular structures.

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