Version 3.4 (R2009b) Bioinformatics Toolbox Software :: Bioinformatics Toolbox Release Notes (Bioinformatics Toolbox)

Version 3.4 (R2009b) Bioinformatics Toolbox Software

This table summarizes what's new in Version 3.4 (R2009b):

New Features and Changes	Version Compatibility Considerations	Fixed Bugs and Known Problems	Related Documentation at Web Site
Yes Details below	Yes—Details labeled as Compatibility Considerations, below. See also Summary.	Bug Reports Includes fixes	Printable Release Notes: PDF Current product documentation

New and updated features in this version include:

Data Format and Database Functions

Following are new functions:

fastainfo — Return information about FASTA file.
fastqinfo — Return information about FASTQ file.
fastqread — Read data from FASTQ file.
fastqwrite — Write to file using FASTQ format.
sffinfo — Return information about SFF file.
sffread — Read data from SFF file.
tgspcinfo — Return information about SPC file.
tgspcread — Read data from SPC file.

The following functions are updated:

affyread — Read microarray data from Affymetrix^® GeneChip^® file. Updated to read cell layout files (CLF) and background probe (BGP) files.
multialignwrite — Write multiple alignment to file. Updated to write a file in either ClustalW ALN format (default) or MSF format.

Protein Analysis Functions

Following is a new function:

isotopicdist — Calculate high-resolution isotope mass distribution and density function.

The following function is updated:

cleave — Cleave amino acid sequence with enzyme. Updated to let you specify an exception to the enzyme's cleavage rule and to let you specify a maximum number of missed cleavage sites. Also updated to return the number of missed cleavage sites per peptide fragment.

Data Visualization Functions

The following functions are updated:

microplateplot — Display visualization of microtiter plate. Display updated so that first row of input matrix appears at the top and is labeled row A. Updated to return the handle to the axes of the plot, which lets you reverse the order or the rows or columns in the display. Updated to include a new property, 'TextFontSize', which lets you control the font size of text labels.
multialignviewer — Display and interactively adjust multiple sequence alignment. Updated to accept a list of names to label the sequences in the Multiple Sequence Alignment Viewer window.
showalignment — Display color-coded sequence alignment. Updated to control the inclusion or exclusion of terminal gaps from the count of matches and similar residues when displaying a pairwise alignment.

Compatibility Considerations

In Bioinformatics Toolbox™ Version 3.3, the default layout for the plot returned by microplateplot displayed the first row of the input matrix at the bottom.

In Bioinformatics Toolbox Version 3.4, the plot displays the first row of the input matrix at the top.

Sequence Statistics Functions

The following function is updated:

seqshowwords — Graphically display words in sequence. Updated to search for multiple words in a sequence.

Sequence Utility Functions

The following functions are updated:

cleave — Cleave amino acid sequence with enzyme. Updated to let you specify an exception to the enzyme's cleavage rule and to let you specify a maximum number of missed cleavage sites. Also updated to return the number of missed cleavage sites per peptide fragment.
rebasecuts — Find restriction enzymes that cut nucleotide sequence. Updated to use Version 904 of REBASE^®, the Restriction Enzyme Database.
restrict — Split nucleotide sequence at restriction site. Updated to use Version 904 of REBASE, the Restriction Enzyme Database.

Sequence Visualization Functions

The following functions are updated:

multialignviewer — Display and interactively adjust multiple sequence alignment. Updated to accept a list of names to label the sequences in the Multiple Sequence Alignment Viewer window.
showalignment — Display color-coded sequence alignment. Updated to control the inclusion or exclusion of terminal gaps from the count of matches and similar residues when displaying a pairwise alignment.

Pairwise Sequence Alignment Functions

Following is a new function:

localalign — Return local optimal and suboptimal alignments between two sequences.

The following functions are updated:

multialignviewer — Display and interactively adjust multiple sequence alignment. Updated to accept a list of names to label the sequences in the Multiple Sequence Alignment Viewer window.
showalignment — Display color-coded sequence alignment. Updated to control the inclusion or exclusion of terminal gaps from the count of matches and similar residues when displaying a pairwise alignment.

Multiple Sequence Alignment Functions

The following functions are updated:

multialignviewer — Display and interactively adjust multiple sequence alignment. Updated to accept a list of names to label the sequences in the Multiple Sequence Alignment Viewer window.
multialignwrite — Write multiple alignment to file. Updated to write a file in either ClustalW ALN format (default) or MSF format.
showalignment — Display color-coded sequence alignment. Updated to control the inclusion or exclusion of terminal gaps from the count of matches and similar residues when displaying a pairwise alignment.

Phylogenetic Tree Tools and Methods

The Phylogenetic Tree Tool includes the following updates:

Includes two new circular print renderings: equal angle and equal daylight
Updates to Tools menu, including commands to select specific branch and leaf nodes based on different criteria, such as distance, common ancestors, leaves only, and descendants.

Following is a new method:

cluster — Validate clusters in phylogenetic tree.

The following method is updated:

plot — Draw phylogenetic tree. Updated to include two new algorithms for circular layouts: equal angle and equal daylight. Updated to let you rotate circular trees from 0 through 360 degrees and to rotate leaf labels of circular trees so that the text is aligned to the root node. Updated the 'LeafLabels' property so that it defaults to true for circular layouts and to false for square and angular layouts.

Compatibility Considerations

In Bioinformatics Toolbox Version 3.3, the 'LeafLabels' property defaulted to true when the 'Type' property was 'square' or 'angular', and to false when the 'Type' property was 'radial'.

In Bioinformatics Toolbox Version 3.4, the 'LeafLabels' property defaults to false when the 'Type' property is 'square' or 'angular', and to true when the 'Type' property is 'radial'.

Clustergram Window

The Clustergram window has two new toolbar buttons:

Annotate button — Shows and hides intensity values for each area of the heat map.
Show Dendrogram button — Shows and hides the dendrograms.

Clustergram Methods and Properties

The following are new methods of a clustergram object:

addTitle — Add title to clustergram.
addXLabel — Label x-axis of clustergram.
addYLabel — Label y-axis of clustergram.
clusterGroup — Select cluster group.

The following properties of a clustergram object are renamed:

ColumnMarker is now ColumnGroupMarker.
Impute is now ImputeFun.
Ratio is now DisplayRatio.
RowMarker is now RowGroupMarker.
SymmetricRange is now Symmetric.

Note The former property names are still valid.

Following is a new property related to the display of dendrogram tree diagrams in a clustergram object:

ShowDendrogram

The following are new properties related to the display of row and column labels of a clustergram object:

RowLabels
ColumnLabels
RowLabelsLocation
ColumnLabelsLocation
RowLabelsColor
ColumnLabelsColor
LabelsWithMarkers
RowLabelsRotate
ColumnLabelsRotate

The following are new properties related to annotating data in a clustergram object:

Annotate
AnnotColor
AnnotPrecision

When using clustergram properties with the get and set methods, the property names are now case sensitive.

Compatibility Considerations

In Bioinformatics Toolbox Version 3.3, the property names of a clustergram object were not case sensitive when used with the get and set methods.

In Bioinformatics Toolbox Version 3.4, property names of a clustergram object are case sensitive.

HeatMap Object, Methods, and Properties

Following is a new object:

HeatMap object — Object containing matrix and heat map display properties.

The following are methods of a HeatMap object:

addTitle — Add title to heat map.
addXLabel — Label x-axis of heat map.
addYLabel — Label y-axis of heat map.
plot — Render heat map for object.
view — Render heat map for object.

A HeatMap object includes many properties that control the creation of the heat map, row and column labels, axes labels, title, and data annotation.

DataMatrix Methods

Following is a new method of a DataMatrix object:

dmwrite — Write DataMatrix object to text file.

Microarray Functions, Objects, Methods, and Properties

Following are new functions to create objects containing data from a microarray gene expression experiment:

bioma.ExpressionSet — Contain data from microarray gene expression experiment.
bioma.data.ExptData — Contain expression data from microarray gene expression experiment.
bioma.data.MetaData — Contain sample or feature metadata from microarray gene expression experiment.
bioma.data.MIAME — Contain experiment information from microarray gene expression experiment.

These objects have properties and methods that are useful for viewing and analyzing the data or a subset of the data.

Mass Spectrometry Functions

Following are new functions:

isotopicdist — Calculate high-resolution isotope mass distribution and density function.
tgspcinfo — Return information about SPC file.
tgspcread — Read data from SPC file.

The following function is updated:

mspeaks — Convert raw peak data to peak list (centroided data). Updated to include a new property, 'Style', which lets you specify the style for marking the peaks in the plot.