PProdigal: Parallelized gene prediction based on Prodigal. This is just a small wrapper around the prodigal gene prediction program that splits input into chunks and processes them im parallel, since prodigal does not support multithreading by itself. The wrapper supports all command line parameters ...
The 48 layer deep CNN architecture Inception v3 [31] was implemented in Python using Keras with TensorFlow backend and GPU hardware (Nvidia RTX 2080 ti). The image tiles (and particularly each pixel in the tiles) were used as features for the prediction. The response variables used were the...
forlineinopen("test.genepred"): gene = line.rstrip().split('\t') exons.extend([(int(s),int(e),gene[1])fors,einzip(gene[8].rstrip(',').split(','),gene[9].rstrip(',').split(','))]) exons = sorted(exons,cmp=cmpBed) printsum([bed[1]-bed[0]forbedinmergeBed(exons)])...
包括了所有物种的参考序列(e.g., gene prediction、transcript prediction等) 而从中再引申出来的“GenBank”,则是所有researcer都可以上传自己研究得到的sequence About RefSeq The Reference Sequence (RefSeq) collection provides a comprehensive, integrated,non-redundant, well-annotated set of sequences, including...
Using the original binary cross-entropy loss function would result in a bias in data prediction toward the side with more samples, given the unbalanced nature of our positive and negative dataset. To address this issue, we attached weights of different multiples to the positive set. The modified...
How noncoding DNA determines gene expression in different cell types is a major unsolved problem, and critical downstream applications in human genetics depend on improved solutions. Here, we report substantially improved gene expression prediction accur
Studies have shown its power in image classification and tumor subtype prediction. However, multimodal DBN has not been used in predicting disease-gene associations.In this study, we propose a method to predict disease-gene associations by multimodal DBN (dgMDL). Specifically, latent representations ...
Genome Sequencing Location Prediction Aim To develop and deploy a sophisticated and user-friendly web application capable of predicting the origin or spread location accurately based on genomic sequences. By combining robust AI/ML models, efficient backend systems, and an intuitive frontend interface, ...
Factor analysis decomposes single-cell gene expression data into a minimal set of gene programs that correspond to processes executed by cells in a sample. However, matrix factorization methods are prone to technical artifacts and poor factor interpretability. We address these concerns with Spectra, an...
A prediction model for differential gene expression (DE) based on genome-wide regulatory interactions - stasaki/DEcode