Update to v1.35.0 - New 'Speedy Sequence' nodes and PDB Connector Query Builder Bug Fix

[Vernalis]

We have just updated the nightly build and stable releases for versions 4.5 and 4.6 of the KNIME Analytics Platform to v1.35.0

This introduces 3 new ‘Speedy Sequence’ nodes - nodes which operate on biological sequences without recourse to a bioinformatics toolkit (analogous to our Speed SMILES nodes) - and a minor UI bug fix for the PDB Connector Query Builder node as follows:

1. Speedy Sequence to SMILES
   This node was released following a recent forum request. The node allows conversion of a sequence in single-letter form to a SMILES representation. The sequence can represent any of Protein/Peptide, DNA, RNA, LNA (Locked Nucleic Acid) or PNA (Peptide Nucleic Acid)

Peptide reader

Hi, What’s the best way to read sequences of short peptides and convert them to SMILES(?) to further calculate descriptors? I tried to upload a FASTA file and use openbabel for conversion, but it interprets the fasta sequence as nucleotides, not amino acids. Tnx

2. Speedy Sequence Analysis
   Reports the count and %age of each sequence letter found in a sequence

3. Speedy Sequence Alignment Visualisation
   This node takes two separate column of aligned pairs of sequences (gaps are represented by a ‘-’ character for each residue gap) and generates an SVG visualisation of the alignment e.g.

   

PDB connector Query Builder node bug fix
Following a recent change to the remote API which is used to populate a dropdown in some of the query type inputs which resulted in nonsense suggestions, this bug is now believed to be fixed.

If you spot any problems, please do let us know.

Thanks

Steve