Sherman Westley

The Recipe for Protein-Based Function Predition and its implementation in the ANNOTATOR Software Environment

Published date : 27 Apr 2016

As biomolecular sequencing is becoming the main technique in life sciences, functional interpretation of sequences in terms of biomolecular mechanisms with in silico approaches is getting increasingly significant. Function prediction tools are most powerful for protein-coding sequences; yet, the concepts and technologies used for this purpose are not well reflected in bioinformatics textbooks. Notably, protein sequences typically consist of globular domains and non-globular segments. The two types of regions require cardinally different approaches for function prediction.

type
Book/Book Chapter
journal
Data Mining Techniques for the Life Sciences, Vol. 1415, pg 477-506,2016, ISBN: 978-1-4939-3570-3

HPMV : Human protein mutation viewer - relating sequence mutations to protein sequence architecture and function changes

Published date : 26 Oct 2015

Next-generation sequencing advances are rapidly expanding the number of human mutations to be analyzed for causative roles in genetic disorders. Our Human Protein Mutation Viewer (HPMV) is intended to explore the biomolecular mechanistic significance of non-synonymous human mutations in protein-coding genomic regions. The tool helps to assess whether protein mutations affect the occurrence of sequence-architectural features (globular domains, targeting signals, post-translational modification sites, etc.). As input, HPMV accepts protein mutations - as UniProt accessions with mutations (e.g.

type
Journal Paper
journal
Journal of Bioinformatics and Computational Biology, Vol. 13, No. 5 (2015), doi: 10.1142/S0219720015500286
Impact Factor
0.783

10 Years for the Journal of Bioinformatics and Computational Biology (2003-2013) - A retrospective

Published date : 14 May 2014

The Journal of Bioinformatics and Computational Biology (JBCB) started publishing scientific articles in 2003. It has established itself as home for solid research articles in the field (~ 60 per year) that are surprisingly well cited. JBCB has an important function as alternative publishing channel in addition to other, bigger journals.

type
Journal Paper
journal
Journal of Bioinformatics and Computational Biology, Vol. 12, Issue 3, June 2014, doi : 10.1142/S0219720014710012

Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently "orphan" viral proteins

Published date : 23 Oct 2013

The genome sequences of new viruses often contain many “orphan” or “taxon-specific” proteins apparently lacking homologs. However, because viral proteins evolve very fast, commonly used sequence similarity detection methods such as BLAST may overlook homologs. We analyzed a data set of proteins from RNA viruses characterized as “genus specific” by BLAST.

type
Journal Paper
journal
Journal of Virology, Jan 2014, Vol. 88, Issue 1, doi: 10.1128/JVI.02595-13
Impact Factor
5.076

Protein Sequence-Structure-Function-Network Links Discovered with the ANNOTATOR Software Suite: Application to ELYS/Mel-28

Published date : 19 Sep 2012

While very little genomic sequence is interpretable in terms of biological mechanism directly, the chances are much better for protein-coding genes that can be translated into protein sequences. This review considers the different concepts applicable to sequence analysis and function prediction of globular and non-globular protein segments. The publicly accessible ANNOTATOR software environment integrates most of the reliable protein sequence-based function prediction methods, protein domain databases and pathway, and protein–protein interaction collections developed in academia.

type
Book/Book Chapter
journal
Computational Medicine - Tools and Challenges, 2012, pg 111-143, ISBN 978-3-7091-0946-5

Tachyon search speeds up retrieval of similar sequences by several orders of magnitude

Published date : 23 Apr 2012

The usage of current sequence search tools becomes increasingly slower as databases of protein sequences continue to grow exponentially. Tachyon, a new algorithm that identifies closely related protein sequences ~200 times faster than standard BLAST, circumvents this limitation with a reduced database and oligopeptide matching heuristic.

type
Journal Paper
journal
Bioinformatics 2012, June 15, Vol 28, Issue 12, Pg 1645-1646