In this paper we present several web-based tools to identify conserved patterns in sequences.
In particular we present details on the functionality of PROMO version 2.0, a program for …

The translatome can be defined as the sum of the RNA sequences that are translated into
proteins in the cell by the ribosomal machinery. Until recently, it was generally assumed that …

During protein evolution, novel domain arrangements are continuously formed. Rearrangements
are important for the creation of molecular biodiversity and for functional molecular …

10.7554/eLife.03523.001 Deep transcriptome sequencing has revealed the existence of many
transcripts that lack long or conserved open reading frames (ORFs) and which have been …

To the Editor—Ribosome profiling (Ribo-seq) has extended our understanding of the
translational ‘vocabulary’of the human genome, uncovering thousands of open reading frames (…

Notch has been linked to β-catenin-dependent tumorigenesis; however, the mechanisms
leading to Notch activation and the contribution of the Notch pathway to colorectal cancer is not …

Kaposi's sarcoma-associated herpesvirus (KSHV; human herpesvirus 8) is associated with
three human tumors, Kaposi's sarcoma, primary effusion lymphoma (PEL), and multicentric …

High throughput RNA sequencing techniques have revealed that a large fraction of the
genome is transcribed into long non-coding RNAs (lncRNAs). Unlike canonical protein-coding …

Background Genomic studies of endangered species provide insights into their evolution and
demographic history, reveal patterns of genomic erosion that might limit their viability, and …

Single amino acid repeats are prevalent in eukaryote organisms, although the role of many
such sequences is still poorly understood. We have performed a comprehensive analysis of …