BioServices.net: September 2005

BioWeka 0.3 and XML-Stylesheets 0.2 offer these new features:

Classifying DNA/RNA sequences using a reimplementation of Eclat (based on codon usage and SVMs)
Merge multiple data sets and store relation names in a nominal attribute
Classification based on heuristic alignments using BLAST or PSI-BLAST
Classification based on global alignments using an implementation of the Needleman-Wunsch algorithm, implemented by Andreas Dräger
Cut DNA/RNA sequences after the first stop codon
Calculate the open reading frames of DNA/RNA sequences
Extracting internal microarray data from MAGE-ML files
Load tab-delimited microarray data (e.g. TIGR's tav, mev and Stanford as well as spot format) into Weka
Transform score alignments depending on the instance weight and the alignment rank
Bug fixes for JAligner, Loader classes and many more

Martin Szugat (BioWeka main developer)

The current issue of the German XML magazine publishes these articles among others:

Review of the book XML for Bioinformatics: Little theory, much practice!
BPEL Maestro: Orchestration of bioinformatics Web Services (ProThesaurus and LiMB) using BPEL Maestro from Parasoft.

BioWeka 0.2 offers these features:

Loaders and Savers for the sequence formats: FASTA, GenBank, EMBL and Swiss-Prot
Classifiers based on sequence alignment: local and secondary structure element alignment
Evaluators to transform (alignment) scores into (pseudo) likelihoods: average, sum and maximum score based as well as rank-based evaluators
Filters for sequence data: RNA/DNA to amino acid translator, RNA to DNA transcriber, DNA/RNA complement and reverse complement translator, symbol counter, e.g. for codon usage analysis, sequence analysis, e.g. calculate average pK values or different amino acid indices based on the AAindex matrices
Normalizers to normalize feature vectors, e.g. codon usage vectors: sum, min-max and standard distribution normalization

Martin Szugat (BioWeka main developer)

BioServices.net