Bioinformatics Toolbox 3.5

Sequence Analysis Software

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

Sequence Alignment

Bioinformatics Toolbox offers a comprehensive set of sequence analysis software methods for performing 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

You can manipulate and analyze your sequences to gain a deeper understanding of your data. Bioinformatics Toolbox sequence analysis software lets you:

• 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

Bioinformatics Toolbox sequence analysis software contains tools for visualizing 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 view, modify, and explore pairwise and multiple sequence alignments.

Phylogenetic Tree Analysis

Bioinformatics Toolbox sequence analysis software 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 UPGMA.

Bioinformatics Toolbox sequence analysis software includes tools for weighting and rerooting trees, calculating subtrees, and calculating canonical forms of trees. Through the graphical user interface (GUI), you can 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

Bioinformatics Toolbox provides several protein sequence analysis software methods, as well as 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. A GUI lets you view properties along the length of your sequence. Bioinformatics Toolbox sequence analysis software also contains a Molecule Viewer tool for displaying and manipulating 3-D molecular structures.