[HTML][HTML] lincRNAs: genomics, evolution, and mechanisms
Long intervening noncoding RNAs (lincRNAs) are transcribed from thousands of loci in
mammalian genomes and might play widespread roles in gene regulation and other cellular …
mammalian genomes and might play widespread roles in gene regulation and other cellular …
Multiple sequence alignment modeling: methods and applications
M Chatzou, C Magis, JM Chang… - Briefings in …, 2016 - academic.oup.com
This review provides an overview on the development of Multiple sequence alignment
(MSA) methods and their main applications. It is focused on progress made over the past …
(MSA) methods and their main applications. It is focused on progress made over the past …
Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts
It is a challenge to classify protein-coding or non-coding transcripts, especially those re-
constructed from high-throughput sequencing data of poorly annotated species. This study …
constructed from high-throughput sequencing data of poorly annotated species. This study …
FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome
Whole transcriptome sequencing (RNA-seq) has become a standard for cataloguing and
monitoring RNA populations. One of the main bottlenecks, however, is to correctly identify …
monitoring RNA populations. One of the main bottlenecks, however, is to correctly identify …
High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing
Accurate annotation of genes and their transcripts is a foundation of genomics, but currently
no annotation technique combines throughput and accuracy. As a result, reference gene …
no annotation technique combines throughput and accuracy. As a result, reference gene …
Computational analysis of conserved RNA secondary structure in transcriptomes and genomes
SR Eddy - Annual review of biophysics, 2014 - annualreviews.org
Transcriptomics experiments and computational predictions both enable systematic
discovery of new functional RNAs. However, many putative noncoding transcripts arise …
discovery of new functional RNAs. However, many putative noncoding transcripts arise …
ITS2, 18S, 16S or any other RNA—simply aligning sequences and their individual secondary structures simultaneously by an automatic approach
Secondary structures of RNA sequences are increasingly being used as additional
information in reconstructing phylogenies and/or in distinguishing species by compensatory …
information in reconstructing phylogenies and/or in distinguishing species by compensatory …
piRNAs and their functions in the brain
Piwi-interacting RNAs (piRNAs) are the non-coding RNAs with 24-32 nucleotides (nt). They
exhibit stark differences in length, expression pattern, abundance, and genomic …
exhibit stark differences in length, expression pattern, abundance, and genomic …
Detection of long non–coding RNA homology, a comparative study on alignment and alignment–free metrics
TMR Noviello, A Di Liddo, GM Ventola, A Spagnuolo… - BMC …, 2018 - Springer
Abstract Background Long non-coding RNAs (lncRNAs) represent a novel class of non-
coding RNAs having a crucial role in many biological processes. The identification of long …
coding RNAs having a crucial role in many biological processes. The identification of long …
PlncRNADB: a repository of plant lncRNAs and lncRNA-RBP protein interactions
Background: Long noncoding RNAs (lncRNAs) are endogenous noncoding RNAs,
arbitrarily longer than 200 nucleotides, that play critical roles in diverse biological processes …
arbitrarily longer than 200 nucleotides, that play critical roles in diverse biological processes …