| Bioinformatics Toolbox 1.1 Release Notes | |
This section summarizes the new features and enhancements introduced in the Bioinformatics Toolbox 1.1.
New functions for phylogenetic tree creation and analysis.
phytreeread — Read a Newick formatted tree file into the MATLAB workspace and return a phytree object with data from the file. Data in the file uses the Newick (New Hampshire) format for describing trees.
phytreewrite — Copy the contents of a phytree object from the MATLAB workspace to a file.
phytreetool — Interactive GUI that allows you to view, edit, and explore phylogenetic tree data. This GUI allows branch pruning, reordering, renaming, and distance exploring. It can also open or save Newick formatted files.
seqlinkage — Construct a phylogenetic tree from pairwise distances.
seqpdist — Calculate the pairwise distance between biological sequences.
New object for manipulating phylogenetic tree data.
phytree — Function to create a phytree object.
phytree/get — Get property values from a phytree object
phytree/getbyname — Get node names from a phytree object.
phytree/pdist — Calculate the patristic distances between pairs of leaf nodes.
phytree/plot — Draw a phylogenetic tree object in a MATLAB figure window as a phylogram, cladogram, or radial tree.
phytree/prune — Remove nodes from a phylogenetic tree.
phytree/select — Select branches and leaves from a phylogenetic tree using a specified criteria.
phytree/view — Opens a phylogenetic tree in a phytreetool window.
Updated Hidden Markov Model profile functions
The model structure, that HMM functions use, now includes loop and null transition probabilities. You can read null and loop probabilities from PFAM files using pfamhmmread and from PFAM web databases using gethmmprof..
When the function hmmprofstruct builds an HMM model, the loop and null transition probabilities default to pre-defined values. If necessary, you can later modify the probabilities using the same function.
hmmprofalign includes two new properties to control the scoring of flanking states and null transition probabilities. In addition, a third output argument with indices pointing to the respective symbols of the query sequence was added.
Updated functions (aminolookup, baselookup) to get IUB/UPAC character codes, integer codes, and names for nucleotides and amino acids.
New functions (blastncbi, blastread, getblast) BLAST sequences and view results from within MATLAB.
Updated function (clustergram) to do two way bi-clustering.
New function (imageneread) to read microarray data from an ImaGene Results file. Other functions read microarray data from Affymetrix GeneChip files (affyread) and GenePix Results (GPR) files (gprread).
New function (mapcaplot) to create a Principal Component plot of expression profile data
New function (isoelectric) for protein analysis. Estimate the isoelectric point (the pH at which the protein has a net charge of zero) for an amino acid sequence and estimate the charge for a given pH.
New function (seqdisp) formats sequence output for easy viewing.
Enhanced function (seqdotplot) now returns a second output (the matrix of matches as a sparse matrix).
New function (seqmatch) to find matches for every string in a library.
Bicluster demo — Demonstrates some of the options of the clustergram function.
Bioperl demo — Illustrates the interoperability between MATLAB and Bioperl - passing arguments from MATLAB to Perl scripts and pulling BLAST search data back to MATLAB
Phytree demo for Hominidae species— A phylogenetic tree is constructed from mtDNA sequences for the Hominidae taxa (also known as pongidae). This family embraces the gorillas, chimpanzees, orangutans and the humans.
Phytree demo for HIV/SIV — Analyzes the reconstruction of phylogenetic trees from infected HIV/SIV organisms.
The Bioinformatics Toolbox 1.1 includes several bug fixes made after the version 1.0 release.
For Hidden Markov Model profiles, the emission probability for the first symbol in the profile is now correct. Previously the emission probability did not include null transition probabilities. Ignoring the null transition probabilities caused a small difference in the answer.
When opening the MATLAB Help browser or a function that users the browser, to display results, a number of exceptions are written to the MATLAB Command Window. These exculpations do not affect viewing information in the browser window.
However, in the left pane, the text labels for the tabs are missing. These tabs are, from left t right, Contents, Index, Search, Demos, and Favorites.
To view documentation for the Bioinformatics Toolbox, open a Web browser (for example, IE or Netscape), and enter the address.
http://www.mathworks.com/access/helpdesk/help/toolbox/bioinfo/
| | Bioinformatics Toolbox 1.1.1 Release Notes | Bioinformatics Toolbox 1.0 Release Notes | |
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