conclusions sequence and structural diversity of the 3'utr variable region and poly u/uc region found in the local isolates indicate specificity in the regulating elements of 3'utr that might be associated with differential replication efficacy of the hcv pakistani isolates. the study necessitates functional characterization of these regulating elements to elucidate variable viral eff...

Minimal absent words (MAW) of a genomic sequence are subsequences that are absent themselves but the subwords of which are all present in the sequence. The characteristic distribution of genomic MAWs as a function of their length has been observed to be qualitatively similar for all living organisms, the bulk being rather short, and only relatively few being long. It has been an open issue whet...

As the number of sequenced genomes increases, the ability to deduce genome function becomes increasingly salient. For many genome sequences, the only annotation that will be available for the foreseeable future will be based on computational predictions and comparisons with functional elements in related species. Here we discuss computational approaches for automated genome-wide annotation of f...

The translation of many maternal mRNAs is regulated by dynamic changes in poly(A) tail length. During maturation of Xenopus oocytes, polyadenylation is mediated by three different cis elements in the 3' untranslated region (UTR) of maternal mRNAs. In this issue, Piqué et al. (2008) explore the interplay of these elements to elucidate a combinatorial code that predicts the timing of polyadenylat...

We study the length distribution of a particular class of DNA sequences known as the 5' untranslated regions exons. These exons belong to the messenger RNA of protein coding genes, but they are not coding (they are located upstream of the coding portion of the mRNA) and are thus less constrained from an evolutionary point of view. We show that in both mice and humans these exons show a very cle...

A second case has been found of a nematode gene involved in developmental timing that encodes a short, non-coding RNA. Both RNAs are expressed at specific times and appear to repress target genes by interacting with their 3' untranslated regions. A coincidence? Or does this pathway attract small RNA regulators?

Patterns of similarity between genomes of related species reflect the distribution of selective constraint within DNA. We analyzed alignments of 142 orthologous intergenic regions of Caenorhabditis elegans and Caenorhabditis briggsae and found a mosaic pattern with regions of high similarity (phylogenetic footprints) interspersed with non-alignable sequences. Footprints cover approximately 20% ...

MicroRNAs (miRNAs) are small non-coding RNAs that inhibit gene expression by binding to the 3' untranslated region (3'-UTR) of their target mRNAs. Recent studies show that miR-497 plays an important role in various cancers. Here, we summarize the existing studies of miR-497 as following: (1) miR-497 expression in cancer; (2) regulation mechanisms of miR-497 expression; (3) function of miR-497 i...

Large-scale analysis of the GC-content distribution at the gene level reveals both common features and basic differences in genomes of different groups of species. Sharp changes in GC content are detected at the transcription boundaries for all species analyzed, including human, mouse, rat, chicken, fruit fly, and worm. However, two substantially distinct groups of GC-content profiles can be re...

MicroRNAs form one of the groups of small noncoding RNA molecules that have completely changed our understanding of gene regulatory networks. Because microRNAs have been discovered only relatively recently, most of their functions remain unknown, providing a challenge to both experiment and theory. I review several computational approaches pursued in our group to answer this challenge. In parti...