An area of research in the field of bioinformatics deals with the identification of similarities within one, or between two DNA sequences. Current techniques are quite slow and many matches are missed. The invention provides a faster and more sensitive solution, by using "optimised spaced seeds"...
Exploiting sequence–structure–function relationships in biotechnology requires improved methods for aligning proteins that have low sequence similarity to previously annotated proteins. We develop two deep learning methods to address this gap, TM-Vec and DeepBLAST. TM-Vec allows searching for structure–...
To compare the speed of the HHsearch versions, we randomly selected 1 644 sequences from Uniprot (release 2015_06), built profile HMMs, and measured the total run time for searching with the 1644 query HMMs through the PDB70 database (version 05Sep15). The PDB70 contains profile HMMs for...
A number of factors contribute to the quality of an X-ray structure. The first factor relates to the intrinsic crystal properties and its diffraction capabilities, which is mostly evaluated in term of resolution. The quality metrics used in X-ray crystallography fall into three categories: 1) to...
After searching the most similar sequence of contigs in NCBI NR and Swiss-Prot databases, the GO annotations for the best hits are used to provide functional annotations for the assembled contigs. For all contigs hitting the same transcript in NR database, PARRoT quantify the expressions from ...
Protein Structural Bioinformatics: An Overview Homology Modeling Homology modeling, also known as comparative modeling, is based on the biological fact that when two sequences share high similarity/identity, their respective structures are also similar. In this method, the 3D structure of a protein is...
Homology modeling Machine learning Protein 3D structure Structural bioinformatics Collective intelligence Artificial intelligence 1. Introduction The protein folding problem has become an integral part of modern biology; with a historical tale that began nearly over half a century ago. Proteins are diverse ...
TimeLogic Corporation, Decypher bioinformaticsacceleration solution (2002), http://www.timelogic.com/products.html Puttegowda, K., Worek, W., Pappas, N., Dandapani, A., Athanas, P.: A Run-Time Reconfigurable System for Gene-Sequence Searching. In: International VLSI Design Conference (to ...
In: Gu J, Bourne PE (eds) Structural bioinformatics, 2nd edn. Wiley, New York, pp 561–573 Google Scholar Zehr J, Mellon T, Hiorns W (1997) Phylogeny of cyanobacterial nifH genes: evolutionary implications and potential applications to natural assemblages. Microbiology 143(4):1443–1450 CAS...
This oncogenic role is also supported by available bioinformatic databases, as the expression profile of PHLDB3 obtained from several bioinformatics database implies that PHLDB3 might play an oncogenic role (Fig. 3)25,26,27. Additionally, by searching the database GenomeRNAi31, we found out ...