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Updated: Feb 8, 2026

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
Published on: June 8, 2020
Fast sequence analysis based on diamond sampling
Liangxin Gao1, Wenzhen Bao1, Hongbo Zhang1
1Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University, Shanghai, China.
Abstract:
Both in DNA and protein contexts, an important method for modelling motifs is to utilize position weight matrix (PWM) in biological sequences. With the development of genome sequencing technology, the quantity of the sequence data is increasing explosively, so the faster searching algorithms which have the ability to meet the increasingly need are desired to develop. In this paper, we proposed a method for speeding up the searching process of candidate transcription factor binding sites (TFBS), and the users can be allowed to specify p threshold to get the desired trade-off between speed and sensitivity for a particular sequence analysis. Moreover, the proposed method can also be generalized to large-scale annotation and sequence projects.
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