Long intergenic noncoding RNA identification software tools | RNA sequencing data analysis
Long intergenic noncoding RNAs (lincRNAs) have emerged as critical participators in gene regulation in myriads of cell types. The development of the whole transcriptome sequencing technology, or RNA-seq, has enabled novel lincRNA detection, but the bioinformatics analysis toward distinguishing reliable ones remains a challenge.
Assists in the determination of regions of suspected RNAs using information obtained from the RNA of interest. PsRNA is a computing engine for locating all such functionally important regions in prokaryotic genomes. It can be used to fish out regions of interest based on the KEGG Orthology (KO) information collected from positive training data.
Assists for lincRNA prediction with a deep-learning method. lincRNA_predict is a two-layer deep neural network designed for the lincRNA detection and is based on DNA genome analysis. This software exploits the latest findings of lincRNA data set and apply an auto-encoder algorithm to extract the features and the information correlation along DNA genome sequences of lincRNA transcription sites.
Classifies the identification of lincRNAs. iSeeRNA is implemented for high throughput screening of lincRNAs from transcriptome sequencing data. This tool demonstrates high prediction accuracy and runs several magnitudes faster than other similar programs. It can be integrated into the transcriptome data analysis pipelines or run as a web server, thus offering a valuable tool for lincRNA study. A public available webserver for iSeeRNA is also provided for small size dataset.
Furnishes solution for calculating co-expression networks of lincRNAs and protein-coding genes. LINC includes biological terms associated with the sets of protein-coding genes for determining the biological contexts of lincRNAs according to the 'guilty by association' approach.
Provides a simple position weight matrix (PWM)-based strategy for the discovery of intergenic small RNAs (sRNAs) genes. sRNAscanner is a method that predicts large numbers of potential sRNA genes in diverse bacterial species. It also hints at the broader power of customized PWMs as a generic strategy for detection of defined genomic features in diverse bacterial genomes.
An integrative bioinformatics pipeline to facilitate the discovery of bona fide novel lincRNAs that are suitable for further functional characterization. Specifically, sebnif is the only pipeline that implements an algorithm for identifying high-quality single-exonic lincRNAs that were often omitted in many studies.
Classifies expressed lincRNA in next generation RNA sequencing data. ICQ-lincRNA provides an annotation feature for neighboring protein-coding genes and a chromatin map status in nine human celle lines from ENCODE project. This tool handles downstream quantitative analyses including gene count, exon count, overlap with known lincRNAs annotated by GENCODE V12 and Broad lincRNA Catalog.